Sounds like a hassle. Good controller support would beat touch controller in both ergonomics and speed every day.
I hope the Controller support been improved with this launch as I tried to play Factorio on my Steam Deck before but felt like it was just "emulated mouse" support basically which isn't nearly nice enough. I feel like Tropico-series did a good implementation of top-down+strategy controller for their games.
Unfortunately the steam deck touch calibration is kind of bad. Mine is all over the place at times, and on kb/mouse designs it can be hard to be accurate enough.