I don't think artificial scarcity is the reason.
I think Hasbro had no faith that this line would sell at all, so they got Target to support the line by carrying exclusives that wouldn't see the light of day without exclusivity. The deal they made with Target would be for a certain duration, possibly for three waves of Cobra Island; well past the point that Hasbro discovers these are a huge hit, and the characters exclusive to these waves was locked in before release.
It's also possible that the amount Hasbro could make of the exclusives is limited by the deal with Target (Target only bought a specific amount and doesn't care if fans want more).
Hasbro re-releasing the Trooper with accessories removed and different paint apps could be caused by the contract with Target; Target exclusives must be unique in some way from future regular releases.
The situation sucks, and might suck in the possible third wave of Cobra Island.
This is all true.
Hasbro has done Exclusive deals with Wal-Mart, Target, and Walgreens (and formerly Toys R' Us as well). If you're a Star Wars Black Series or especially a Marvel Legends collector, you'll know this. I don't collect either (except for a few Spider-man figures) but Hasbro has established a symbiotic relationship with big box retailers for years. They tend to buy the 'bulk' of their product so it's in Hasbro's interest to keep this relationship.
I thought we all discussed this before - but the intent of the exclusives is to draw you into the store IN THE HOPE you will buy MORE than just your exclusive figure. It is a business strategy. And having a troop builder will incentivize most for repeat business. Suddenly that Target visit you did one-to-three times a month becomes one-to-three times a week, oh and you also buy your groceries there cause they have it and you don't want to go to the supermarket after grabbing your Viper. Most people want a few troop builders rather than just 1 or 2, so they'll keep coming back to get them.
Also with the Exclusives and contracts, Target is possibly ponying up manufacturing costs, etc. so Hasbro is beholden to them or would breach their contract. Specific order numbers and such can even be in there. I'm sure Target has to meet a "minimum" but what does it say about Hasbro producing more? Who knows. Why aren't they making more? Do they even WANT to make more? Maybe they do but the contract won't let them. We'll see as time goes by. I think Hasbro certainly wants more out there, that's more orders for them, but if Target and the contract restrict them right now...there's not much they can do.
Some of the Hasbro G.I. Joe Classified team did a podcast with a group of guys called "Toy Wizards". They did exclaim that the sudden popularity of the line DID catch them all off-guard. They were never really asked about the distribution issues short of comments about how COVID did affect things.
Hasbro has a weird relationship with G.I. Joe. I have mentioned this before but it has been a difficult decade to promote a line that can be described as "pro-war" or "glorifying war and guns, etc." Hasbro is very much still scared of advocacy groups that are constantly watching their products...why do you think most of the guns don't look like real guns?
In addition, Hasbro nosedived G.I. Joe a few years back. A little history lesson: things were "going good" with the 25th Anniversary line and then Rise of Cobra came out. Hasbro focused the toyline around it and the movie performed poorly. A lot of fans weren't happy with it and figures matched the poor character designs. They continued with "Pursuit of Cobra" and tried to incorporate some 25th/30th Anniversary versions of characters on different cardbacks rather than the classic redo ones fans loved. Renegades was a good show but who the hell had "the hub" network? Retaliation came out and though it was a little better...the damage was done to both the franchise and the toyline. Hasbro had also went "all-in" on a movie focus and then started releasing repaints of various figures cobbled together from the 25th Anniversary styling. The *only* option for figures that were getting the 25th Anniversary attention was the Official G.I. Joe Club's "Figure Subscription Service". But because this worked directly with Hasbro and serviced a small pool of Joe fans in a "Direct-to-Consumer" model (much like the first DTC after VvV)...the figures/sets were all around $50 or more/a piece. Hasbro did some exclusives with BBTS and continued doing odd 2 or 3 figure packs. The figures were solid, but more re-used parts, etc. etc. and 2016 was the LAST year Hasbro released any G.I. Joe to retail. The ONLY G.I. Joe figures out after that were part of the Official G.I. Joe Club's subscription line...which as I noted before was expensive since they contracted directly to Hasbro. I think 2018 was the last run of subscription figures and in 2019, the Official G.I. Joe club and convention folded.
So Hasbro tanked the recent revival of G.I. Joe with the movies and gradually, fans and collectors lost interest as years went by. The official convention and club (which Hasbro supported and would display products, hold panels, etc.) ended so it was hard to gauge direct fan interest anymore. I think the G.I. Joe comic rights traded hands and it wasn't as "hot" as before. So there were a lot of variables going "against" G.I. Joe. I will say that Hasbro was WELL-AWARE that Joe fans (especially the RAH ones) were always interested in a 6-inch Marvel Legends-style Joe line. I've been to two Joecons and it was always brought up at the Hasbro panels. I guess for Hasbro, the question was...would Joe fans COME BACK to a 6-inch line?
I think to balance some of risk, possibly ignite a little attention, Hasbro went the exclusive route with Target. COVID hit and messed A LOT up, but the line still managed to become a huge hit.
We'll have to see how it goes from here.