I have given this a bit of a thought and would like to share those with you now.
My problem with the OP isnt their opinion, really. I can even understand that some might not like the style and design of the Yokai-items since they're pretty... "special". My problem is really the reasoning they choose and their childish attitude that came with it. Lore? Immersion? By this standards OP couldnt be an Au Ra Dragoon -> Au Ra, because that would conflict with Yugiri hiding her face in FFXIVs very own storyline and dragoon because they're dragonKILLERS in FFXIV while they were friends with the dragons in FFII (where they come from, hello Richard!). The problem here is that OP themself doesnt have a valid argument! "Lore" is such a cheap one, honestly, when there are so many things in this game already that have the potenial to break your immersion (Twintania as a mount, yeah, sure...).
So the question would be: Why does OP doesnt have a problem with those?
And my guess would be: Because they accepted them as part of the game, overlooked them or didnt even thought about them at all. They're raising a few times how important it is for them that things that are added to the game are Final Fantasy related. If thats really their problem, I can only ask them to give the devs the chance and option to change their game and add stuff to it. Without that we would never see any progress (the famour quote from Henry Ford (?) comes to mind: "If I'd asked the customer what they wanted, I would have build a faster horse-drawn carriage [not a car]").
I also have the feeling that OP is a bit... overreacting and hasty with their judgment - seeing how the merchant we can exchange our medals is located in the Gold Saucer, why not assume that its somehow related to the Gold Saucer in general? Which would open the doors for a lot of "explanation" for those fluffy little guys.
And I kinda feel the need to repeat this: Such collabs - even if you consider them "cheap fanservice" (and apparently not fanservice that you like, thats okay, I didnt liked the FFXI-event nor the rewards) - are only beneficial for a game that you seem to love and care about.
For the theory that 3.3 was shorter because they spended time with making the Yokai-event... I highly doubt it. They added a LOT with 3.3/3.35 but we're at the end of this patch cylce and they're probably working at the next expansion