As far as I know, both GBPVR.exe and PVRX2.exe behave the same way: All channels are listed in the tv guide. When you press channel +/- in live tv it'll skip non-favourite channels, but you can still type a channel number to go directly to that channel.
If you want to fully hide a channel, and not see it anywhere in the app, then you can disable it in the capture source channel list.
Yes, it will be in the TV Guide. Old versions were exactly the same. You can disable the channel though if you dont want to see it in the TV Guide or anywhere in the app.