It makes it easier to pirate your app if you enable that checkbox. macOS attempts to disable iOS apps when SIP is disabled to prevent this but it's not difficult to bypass [1]. I don't necessarily agree with it but this probably does factor into their decision process.
That couldn’t be the reason. 90% of App Store revenue comes from in app purchases of consumables from games. This came out in the Epic trial.
The rest of the most use apps are front end for services where the app is free. There are very very few one time app purchases on iOS where pirating would make sense