The solution I just implemented in my beta works well.
exactly. it's really important in New games or padded files
If it's the same padding each time or a pattern to it, couldn't you make a script that goes through the file and adds the NON-PADDED offsets to a location in the padding bytes, and then make a script only for importing by using those correct offsets., then make a third script that goes through the file and checks the newly printed offset in the padding, subtract your current offset, then take the new value and print that to the padded offset. then make a batch file for doing it automatically.
This way you could reimport to padded offsets or offsets that don't use actual offsets, but rather only a padding offset from the start of the filedata. anything like that.