Hey guys since this is still a problem I did find a way around it for those tree farms for right now. It can be found here: https://youtu.be/FcrRmz5x890. It will work without the smart saplings also.
I can't confirm this. It seems like 2x2 trees need the surrounding airspace in order to grow, so unfortunately I can't think of a way to test this. If you have direct evidence of this still occurring please do post it here
This does not affect 1.12.2