Skinny slicks pumped up proper hard and full mudguards are essentials for a commuting bike. I defy anyone who says that a suspension fork makes an MTB slower, all else being equal, to prove that with a stopwatch, so don’t worry too much about that, it’s more wheel size, weight and position that make road bikes faster than the lack of a little springing in the forks.
Comfort wise, there’s a bit of simply hardening up and getting used to it but also worth noting that my OH was never truly comfy on her bike until we stopped mucking about with big wide padded saddles and got her a much narrower, firmer, but still female specific one, WTB Deva in her case. It’ll likely be counterintuitive for her but something more like you’d pick for yourself but in a female version will likely be best once shes used to the regular riding. After all, you need to have your weight on your sit bones, not your soft tissues, that’s the same for everyone, and women’s sit bones aren’t all that much further apart than men’s, a couple of cm at most. There’s no reason they should need massive wide saddles, and indeed they are often worse than firmer ones after a few minutes as you sink in and end up putting pressure on areas that you shouldn’t be.