Yeah, this is something I struggle with. To us, the checkpoint seed sort of *is* the character of the TumbleSeed. So it's sort of that in his default state TS plants checkpoints. Haven't talked about this much with other people on the dev team, but it's something I've been mulling over personally.
Yeah, I can totally understand that commitment to the character. Its actually a very interesting conversation to be having and I'd like to hear what other people have to say as well. I think a big argument for changing the default is to appease the nature of roguelikes. By making the default seed the checkpoint seed you're establishing a meta where the beginning of every run begins exactly the same: the player has to switch to a different seed than the one equipped. That sort of goes against the idea of varied gameplay, in a way.
Related: Have you considered starting the player with more crystals so that the approach to the beginning of the first biome, as far as plots go, has more potential for variance?