I've seen some issues reported with the use of rollout.io in the past. Is there any indication that Expo's over-the-air update feature are completely restricted? Or is it more about how you use them (i.e. just performing minor bug fixes and updates and not major app changes).
Are you talking about apps, that were distributed via Appstore? Then you should take a look at Appstore-Review-Guidelines, 2.4.5, (viii): They must use the Mac App Store to distribute updates; other update mechanisms are not allowed.
Every change of a signed binary will break the signature, and apps with an invalid signature won't start.