Plenty of people stream Overwatch, and do stream transitions, without getting banned. If you are not altering inputs to Overwatch it shouldn’t be a problem.
If you have a single macro that does both a scene transition and sends an input to Overwatch, that might be problem so… don’t do that.
The only hotkeys I have set up for OBS are start/stop recording (I don’t stream, I only use OBS to record), but I don’t see why other hotkeys should be different.
Well, I suppose it’s just barely possible that all the streamers that use scene transitions in Overwatch have a 2-PC set up so that OBS, the stream deck, and so on, are all on the capture/streaming PC and not affecting the gaming PC at all. Seems unlikely.
I’m sure you can get a more definitive answer either from our #technical-support forum (possibly) or from a streaming-oriented reddit or the like (almost certainly).