It would be absolutely incredibly godlike uber pwnge if by a miracle we could have a process that would take all the weirdness out(of zoom ,rotate,origins,offsets and import with different image area) by taking a snapshot at the current state(what you view) creating duplicate layers and deleting all the transforms and unifying them into one system of coordinates where everything can connect without having the weirdness of offsets preferably with the added bonus of centering all the origins in one place
But maybe it’s really not possible and I’m just rambling 
I think it’s a reasonable idea, but I don’t know how much the implementation effort would be.
G.