Retouching

You can use PortraitPro for your beauty editing, as long as you do not introduce artefacts. Some of the settings, when pushed, do introduce those. If you turn the hair green for a model, and it looks "natural", go for it. I push professional models more than amateur models, and I've decided, that I don't like the all polished (American) look, PortraitPro produces with some parameters. Since Lightroom introduced its advanced masking I am less inclined to change to PortraitPro and I think that careful editing in Photoshop produces better results. 

Adobe stock accepts any well edited photos, regardless of the tools used. The filter aversion is more against those filters that provide unnatural results. 

I use PortraitPro all the time, primarily to change eye color. Since I run my portraits through a facial restoration program, it always turns irises brown. The same can be accomplished in Photoshop's Camera Raw Filter or other means, but Portrait Pro is faster and provides a varity of colors to choose from. But otherwise I stay away from adding makeup and the like by turning off most if not all of the other features. I learned a long time ago that it's easy to get carried away.

If it really isn't able to be noticed that software has added the makeup, then I don't think it's necessarily out of the question.  Filters tend to be exaggerated and easily noticeable from my experience, and I feel sure that's why they aren't recommended.  I suppose you'll only know if your image additions appear natural enough if you submit a few. 

I wonder if using that software for commercial use is restricted somehow?  I would check the license to be sure.

But if it really is that easy to makeup with software, I also feel confident that an experienced designer would want to add that themselves so they could style the model exactly how they wanted to.  Food for thought!

I don't think PortraitPro qualifies as a "filter". As long as the edits are subtle and realistic and don't end up making your subject look like a plastic doll, I think you'll be okay. Adobe has repeatedly stated that there is a market for "authentic" people doing "authentic" things, so you don't necessarily need to strive for perfection.