What's the best way to keep a GameObject from getting saved?

I have a ton of *child* GameObjects that I generate both in the editor and at runtime. I don't want to save them in the Unity scene file, because I'm using git so they will create tons of data/noise that I don't need at this stage of the project.

I tried using HideFlags.DontSave, but that causes all kinds of issues, because they become undestroyable unless I track them manually... and also it causes CheckConsistency errors, because the parent transform seems to still think it has children,...

What's the best way to keep a GameObject from getting saved?