How do you a) find out which activity uses it, and b) "mess with it"?
It's hard to give a general answer for that, every app is different. Some apps have an activity called webview activity so it's easy enough to find. Just poke around the smali files and try to figure it out. If you can't figure it out on your own it will be pretty hard to explain. You're not gonna have a program that you click on a big "Remove In-App-Browser" button. As for messing around, do whatever you want. Delete lines, add letters, or whatever makes you happy.
I'm getting an error telling me that I can't do anything to a certain app "as it is splitted using google's android app bundle".
Is there a way to get around that?
What is giving you that error and what are you trying to do to the app? You have to be more specific.