First, with semi flat feet, you should use some boot insert. Next, how tight do you tie your boots? You may be over tightening around the balls of your feet as I noticed that your foot pain is greater when you used boas versus using regular laces. Also, I've noticed you listed a few Salomon boots, which normally run a bit narrower in the toe box versus other brands, especially in the F series. It could be a combination of the things I just mentioned causing your pain.
If keeping the laces looser around the balls of your feet with a wider boot with insoles doesn't help, you might want to see a doctor.