I noticed (seemingly after the most recent update) the following:

• placing entity outside of reach with LMB in map view places a ghost entity automatically
• picking up entity outside of reach with RMB marks an entity for deconstruction
• actions above don't save to UNDO stack

I would personally prefer that the default behavior didn't change except allowing for remote configuration and copy/paste . There already are controls for cancelling deconstruction, and it's holding SHIFT with deconstruction planner, so I think adding Shift+RMB is redundant.

I would prefer disabling the auto-ghost building and unmark-deconstruction with shift RMB, because there already are controls for that, and I don't want to accidentally mark some entity for building/deconstructing in a remote place and be unable to UNDO.

As far as I'm aware, I've only added functionality to interactions that don't do anything in vanilla. (LMB with non-ghost cursor in map view and R, Shift+R, RMB, and Shift+RMB in map view or out of range).

The auto-ghost placing should be undoable since all it does is replace the item in cursor with a ghost. The placing of the ghost is done by the game itself.
Rotation and deconstruction requests (R, Shift+R, RMB, and Shift+RMB) are indeed sadly not undoable (see requests here: https://forums.factorio.com/70393 and https://forums.factorio.com/100960). However, I think that I'll soon be able to integrate this with https://mods.factorio.com/mod/redo (which implements its own undo/redo queue entirely in Lua), so that if you're using that mod, they would be undoable.

Yes, you can already cancel deconstruction with the deconstruction planner using shift, but the whole point is that you now don't have to use the deconstruction planner for individual entities since RMB works, so I thought that Shift+RMB would be useful as well, especially since you can't undo it :) If undo support worked, I'd consider removing Shift+RMB.

Seems like you'd like a setting to be able to disable all of this though?

Yeah, it would be useful if there was some toggle for those controls, I think. Something that can allow me to enable/disable certain actions separately.

Currently they are connected to the base game keybinds build, rotate, reverse-rotate, mine, and editor-remove-scripting-object. I suppose I could make them their own controls that can be changed or disabled separately.

You can now disable specific interactions in Settings > Controls :)

Thanks, excellent work, will check later! :)