Hmm... I'm only now testing this, but I just noticed that burner long inserters and long inserters can only fast replace each other, while all the other inserters (both long, burner, and normal) can fast-replace each other. That's weird, I'll have to fix that.
As for the upgrade planner... I'm not sure about that. I didn't realize that was part of vanilla, and the way they have implemented it... I have no idea how it actually works. The 0.16 mod made it easy, by having a button on the GUI and a hotkey for setting what would upgrade into what, but vanilla... as far as I can tell, has nothing like that. I'm not sure how to even use it...
Anyways, I have the fast replace fix ready to upload, but I'm gonna have to look into upgrade planner, figure out how it works before I can implement a fix, and then upload both.