I suppose in theory, .ARE files are okay to put in the override folder, as long as you're changing certain values only.
The only instance where it wouldn't work so well is if it's for a module that uses an .ARE with the same name as another module.
Example: in TSLRCM, the Refugee Landing Pad .ARE is used in the main module as well as the added module where Atton, Bao-Dur, and another party member fight through armies of bounty hunters. In this instance, it would make sense for the whole level to look exactly the same, so anything that you would change in the .ARE file can likely be placed in the override folder without anything going wrong.
Another example: in BoS:SR, there is another Ebon Hawk module for the vision at the beginning of the Solomon's Revenge portion. The values for DynAreaColor, OnEnter, SunFogColor, SunFogFar, SunFogNear, and SunFogOn are different between the two. If you place that particular .ARE in the Override folder, you overwrite both of them. This is what most people like to avoid to ensure compatibility, this is the main reason to just place .ARE files inside module files rather than the Override folder.
I hope this helps.