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

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

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?

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