Yeah, I understand your concerns. In fact, I was modding the official ROM using my microG installer (and maintaining it) for that same reason. Anyway, whenever shit happens, a reverse-migration is likewise possible and I’ll probably develop it if noone does it before.
What it doesn’t sound is reliable (regarding Gobble-dependent apps), as you pointed in 3 and we recommended to some users in the forum. But it is still safer and confortable (long-term) to trust your system to LOS first. You could revert your microG setup at any time with a patched official LOS.
There’s simply no way to patch a pre-odexed ROM, 
. You could (theoretically, I didn’t found a way) de-odex the ROM, then patch. But that’s not an easy-piece task AFAIK and you will need to make an additional step on every single update.
This just occurred to me as I write thanks to you: I don’t know however if you could use Xposed and microG plugins to get microG patches applied over the air on pre-odexed ROMs. I haven’t trusted Xposed historically, but now that the requiring packages are on F-Droid (installer, FakeGapps), that could be a way. Edit: the Xposed Installer on F-Droid just downloads and flash the original Xposed ZIP. Since that’s not built by F-Droid, I won’t trust it rightaway. You’ll need to choose whether you trust random binaries in your system.