Our esteemed colleagues at BWL held an hourlong seminar, complete with Powerpoint presentation and complimentary Vitaminwater and Powerbars*, explaining that UB seems to patch-rename the Crooked Crane's script, which has made a lot of people unhappy and, at least according to them, serves no purpose except some sort of cosmetic fix because the scriptname and the ARxxxx didn't match.
Seminar may be found
here, but the upshot is that they think you should be doing
EXTEND_TOP ~AR0004.bcs~ ~ub/crane/AR0021.BAF~
instead of
EXTEND_TOP ~AR0021.bcs~ ~ub/crane/AR0021.BAF~
COPY_EXISTING ~ar0021.are~ ~override/ar0021.are~ /* Associates correct area script */
WRITE_ASCII ~0x94~ ~AR0021~ /* Corrected Crooked Crane, Level One */
I have not extensively researched the matter, but if they're right, then it certainly seems like a change worth making. In my slightly mangled build I don't see that either AR0021.BCS or AR0004.BCS even exist in the core game to begin with--which is presumably why you felt safe in the first place renaming it, but on the other hand is doubtless why later modders felt perfectly safe using the confusing-but-not-otherwise-invalid AR0004.BCS .
* I am exaggerating, but by less than you think.