I played a whole run of the base game without mods on my Steam Deck in handheld mode and found it just fine. It uses the extra buttons on the back quite effectively.
I think some people set speed run records on the steam deck. Obviously, the number of pixels is lower and the processor isn't as powerful as a desktop, so a megafactory might not work well, but should be fine for tinkering with a design.
Imo it's a little too cumbersome to comfortably play on the deck. Totally possible and it does work thanks to community controller presets but I feel limited playing on the deck compared to when I play on mouse and keyboard and a full size monitor.
The Factorio dev. I've heard he's a shit person but not dove deeper into it.
Edit; did some looking and yeah, he's a shitbag. He claimed that Statutory Rape was a SJW term, and that teachers should be able to seduce their students as long as they weren't violent.
Then he used a dev blog to link to a racist misogynistic jackass, and when called out on it (The guy just wanted a disclaimer on the link) Korvex went on a rant about cancel culture and then tried to defend the misogynistic views, claiming that "maybe there's a reason why there are so few women coders"