Ok found that event id 314 is where the cutscene where the trainers mother asks you to get your stuff. Setting this to 3 unsets this. After doing this cutscene, the value is 5. The value is 13 once post game is complete it looks like.
305 I believe may be the flag that sets the bag icon on the bottom screen menu (as I had only set 314 down to 3 and I still had access to my bag). It's post game value is 26.
It's pre-bag value is 1 and post bag value is 2. I will try setting that one back to see what happens.
EDIT:
After setting 305 back to 1, this retriggers the beggining of game intro scene at the house! But only if I fly to the house. (my bag remains on until I trigger this cutscene)
After I retrigger the meowth waking me up cutscene, my hat and bag are now gone! But I still have my shoes, pants, glasses, and shirt that I had on before I redid the event. I will now try to warp to a different location to avoid triggering the other cutscenes. Then will see if setting the event ids back will preserve my bagless state. Though I may have to go without a hat as well as I have no idea what will happen if I try to put the hat back on in the dressing room when the bag isn't on.
By the way, I still have access to all my bottom screen buttons. It seems those are handled by different event ids.
EDIT2:
Warping did not work. (got the infamous invisible trainer bug hang at the pokecenter. Perhaps trying it somehwere else would have worked better, but it turns out this is not nessecery!)
I reset the event flags. I boot the game while still in my bedroom. Meowth is still there, but after I leave it resets to normal. But I still don't have my hat or bag on!
So looks like bag removable is a success! This likely only requires setting event id 305 to 1 and retriggering the beggining cutscene outside the house. Once you have meowth wake you up, save game and reset event id back to what it was before you edited it. I will se what happens when I go to a dressing room.
EDIT3:
Ok looks like you can still change your clothing. However it becomes impossible to put on a hat or bag. You show up with these items on while in the dressing room UI, but changes to bag/hat are not reflected on the overworld).
I will now see if these changes carry over into battles.
EDIT: Hmm seems that while in battle I still have the default bag on. The hat I had on before I triggered the event is also still on while in battle. I can take the hat off and that change is reflectd on the inbattle model, but the bag remains. But I still have no hat or bag on in the overworld. Seems perhaps there's a special "no bag and hat" flag somewhere in the save that impacts only the overworld model. Interesting.
I guess I'll have to wait till pkHeX has the ability to alter customization settings on the trainer.