Flip coin manufacturing origins
First off, Pokemon Coin Fan has an excellent guide that covers all sorts of background information about the flip coins. Some of the information contained here is also found there.
Bulbapedia also has an article that covers high level information on the coins. Again, some of the information found here is also found there.
Background
In case you didn’t know, a majority of the plastic flip coins are manufactured in Japan. Not only that but the flip coins have been around for as long as the trading cards themselves. The coins manufactured in Japan have consistently been about 30mm in diameter.
Coins have also been manufactured in the United States and China. Product packaging will usually clarify with “Coin made in China” or simply “Made in U.S.A.” applying to the entire product. There are some edge cases where this text may not be reliable.
The 34mm, 41mm, and 51mm coins are all produced in the U.S.A.
Generation 1 and Generation 2
Beginnings within Japan
The very first flip coin to be produced was this Chansey that was released in the Japanese Starter Deck, concurrently with the original Expansion Pack set, in October 1996. It was made of hard black plastic and had a holographic finish on the frontside. With few exceptions, all flip coins produced in Japan have followed this same overall design (hard black plastic, colored/holographic frontside).
There were a few different backsides that were used in generations 1 and 2; the backside that we have today would not be introduced until generation 3.
A note on Gen 1 coin backs
Interestingly, the very first coins released during generation 1 have the text “任天堂 ©C/G/M” on the backside. “任天堂” is Nintendo, the “C” stands for Creatures, the “G” stands for Game Freak, and the “M” stands for Media Factory.
Media Factory was originally responsible for the manufacturing and distribution of the cards within Japan (page 9, line 35).
Later-produced versions of these coins dropped the letter “M”.
The final coins (that we know of) to contain the letter “M” were the Raichu and Gloom coins released with the Kuchiba and Tamamushi City Gym Decks.
Beginnings outside Japan
Wizards of the Coast won the exclusive license to manufacture and distribute the card game outside of Japan.
Base Set was released in January 1999 and alongside it were the Overgrowth, Zap!, Brushfire, and Blackout theme decks. Just like Japan’s Starter Deck, these theme decks included a Chansey coin inside. Unlike in Japan, this coin was made of paper and had a layer of holographic foil printed onto them (in a similar manner to the actual trading cards). All WOTC-made products featured either a paper-based coin or a metal coin.
Paper-based coins with holographic foil
The paper coins were manufactured by WOTC and, presumably, were all made in the U.S.A. (per product packaging only stating “Made in the U.S.A.”).
You can skim through @lyleberr‘s gallery here (forum thread) and here (Imgur album) to view photos of various boxes and verify the country of manufacture text.
Metal coins
WOTC produced their metal coin in Gen I of the TCG and would completely replace the paper coins with metal coins starting in Generation II.
Metal Pikachu coin
This coin was included in the Thunderstorm and Tempest Gift Boxes (2000) and also in the Legendary Collection Lava and Turmoil Theme Decks (2002).
Thunderstorm Gift Box states “Made in the U.S.A. Coin made in Korea” on the box.
Tempest Gift Box also states “Made in the U.S.A. Coin made in Korea”.
Interestingly, the Legendary Collection theme decks only say “Made in the U.S.A.”.
I have not personally opened any of these products, so I do not know if there are any actual differences between the coins released in the Gift Boxes versus the ones released in the Legendary Collection theme decks.
It is possible that the Legendary Collection theme deck packaging does not have the correct text on it. It is also possible that, indeed, the manufacturing process of this Pikachu coin was moved from (South) Korea to the U.S.A. during the two year gap between these product releases.
Metal Lugia coin
This coin was included in all of the theme decks released for the Neo series and Pokemon-e series of theme decks. There are three different variations as documented here.
This coin is somewhat interesting - besides the documented differences in the backside, I also noticed that the Lugia on the frontside is not the same size on any of the three variants. Check out these images from Pokemon Coin Fan: Largest Lugia, Smaller, Smallest.
Anyways, here is the info on the country of manufacture text:
Based upon the above, I would wager that the decks saying “Coin made in Japan” were packaged with the variant with this backside and the “Largest” Lugia on the frontside. I think this might be the case as the backside on the other two variants are more similar and so correlate with a change in manufacture region.
This is just a theory, however, as I have not opened a sealed copy of any Wizards of the Coast theme deck (although I’m sure that I could watch an unboxing video on YouTube to confirm this).
Generation 3
Within Japan
The ADV Expansion Pack debuted in Japan in January 2003 and with it came the Treecko, Torchic, and Mudkip Constructed Starter Decks. These three half decks each featured a different new coin design of one of the three Hoenn starter Pokemon. These three coins featured an entirely brand new backside whose design is still in-use today (albeit with slight modifications).
Outside Japan
End of the WOTC license
As is well known, Wizards of the Coast’s license to manufacture and distribute the trading card outside of Japan ended in 2003 with Pokemon-e Skyridge being the final set released in May 2003 (here is an official announcement from WOTC’s website). Because of this, Skyridge never received a second printing. Both Legendary Collection II and Jamboree were apparently in the works but never saw the light of day. WOTC’s Pokemon Organized Play wound down operations through August 2003 (source).
Pokemon USA and Nintendo take over the TCG outside of Japan
Pokemon USA (now known as The Pokemon Company International) took over manufacturing and Nintendo took over distribution of the card game for North America and also for other regions outside of Japan and North America (this distinction is minor but does exist on some era-specific packaging).
EX Ruby & Sapphire was released in June 2003, a little over one month after the release of Skyridge, and with it came the Ruby and Sapphire theme decks. These theme decks featured coins with the same designs as those from the Japanese Torchic and Mudkip Constructed Starter Decks.
Plastic flip coins debut outside Japan
In fact, not only do these coins feature the same design as their Japanese counterparts, but they’re actually the same coins! The two theme decks read “Made in the U.S.A. Coin made in Japan”.
With few exceptions, from EX Ruby & Sapphire through HS Unleashed all flip coins released worldwide were manufactured in Japan. Not only that but these coins are indistinguishable from the ones distributed within Japan. There are some coins that were only released in Japan (like this Squirtle) and some that were only released outside Japan (like this Gold Treecko).
With this change, for a period of time, all Pokemon flip coins were made under one roof and have the same consistency and quality worldwide.
[Coming soon - coins with mysterious origins, international distribution changes, traditional Chinese-gen 3 cards]
