I wholeheartedly agree! When I got my pdf from the subscription I was excited to play a munitions master, thinking that it was no more overpowered or complicated than many other legal options. I actually found this post when I was thinking of making a similar post.
The only reason I can think of for the hard ban is so that GMs don’t need to learn about the siege weapon subsystem(or, less charitably, so that Paizo doesn’t need to say “no siege weapons other than light mortar innovation” everywhere they currently say “no siege weapons”). IMO it isn’t even a siege weapon if it can’t blow a hole in a stone wall. Why can’t it just be some weird idiosyncratic thing. Keeping the Mr. Torgue class from using its most Mr. Torgue option seems wrong.