I hate to tell you, but once you sort out a decent control scheme it plays really well on the steam deck. There are enough buttons to cover everything, it's mainly case of working out what is most logical to you personally so that you don't have to think about it. Gyros for the mouse, and a mode switch on soft-pull LMB to increase precision help a lot.
I might just try to ignore this comment... My biggest worry is precision in placing things, I make my own blueprints but I normally trying to start from scratch for each new game (just my playstyle, not saying it's good/smart) and it being fiddly on the deck. I played a few games with only mouse support and quickly abandoned them since it got old fast. I know Factorio has great keyboard support though and they do have a Switch version so maybe I'm worrying about nothing. My other worry would be performance since my older laptop has some trouble when my base got large enough (with mods) but maybe I'm just making excuses.
Using the touchpads as a mouse works really well. I like to set them as trackball, but there are multiple options and configurations that one is going to feel good for you.
Any chance you could post a community control scheme that's pretty close? I love factorio but haven't gotten a good intuitive control scheme set up on my deck
It's called Steamdeck Midnight Special by impish. Mouse+gyro on right pad. Various controls on the buttons, left joystick press to enter/exit vehicles and switch modes. Left mouse on left side (not the default swap) and extra precision on a soft pull. Enjoy