I don't want to digress too much, but i wanted to have an NPC alchemist in my game, but it made so little sense that I chose to hand-wave his activities rather than map them mechanically, exactly for that reason...
This is what we did to rebalance Vulgar Alchemy:
Yes the main problem remains the limitation on MT. If S&M discovered by vulgar alchemy were an exception to that limitation, it would change everything. Like how elder runes allow to use MT X philosophiae instead of MT x2, maybe vulgar alchemy should allow S&M discovered by it to go up for MT x philosophiae/2 rounded up instead of MT
Edit: and while writing this, I find it's very thematic since philosophiae is clearly linked to alchemy in A&A. So I may put this as a house rule in my game.