But chess39 is just plain chess with changed initial board states right? That doesn't seem like anything different from the point of view of an algo/bot.

I used to play a bit of chess when I was young too, but never sticked to it nor got good at it either, but the complexity is pretty low relative to other games - specially when we talk about automated/bot scenarios.

In the variant you mention now imagine that every piece can have hundreds of different interactions depending on the other pieces on the table plus other pieces outside the table that the bot can't know for sure - I would imagine it would make the bot much weaker overall and specially against a good player independently from training - it just doesn't seem to make mathematical sense that it wouldn't but it's not my area of research so I can be missing some important thing.