Is it not possible to remap them to something more sensible? Or do the deck controls in general not suit well to a game like factorio?

There are likely community layouts you can try. And you can edit them to suit your needs.

I thought a dev adjusted the game for the steam deck? There was factorio friday facts at some point

I use a mod to remove the character and that has improved the steam deck play massively.

I think its the precision of the select box that does it for me