My final vote would be to correct offset whenever it's necessary, practical and possible, so follow the base rules that we previously discussed:
0. If there is no non zero data in pregap/lead-out, use 0 offset. Unless it's possible to manually detect the write offset with a reasonable degree of certainty, in which case combined offset correction can be used.
1. if there is non zero data in lead-out and that data can be fully shifted out of there (left) without spanning non zero data into pre-gap, correct offset with a minimum shift required
2. if there is non zero data in pre-gap and that data can be fully shifted out of there (right) without spanning non zero data into lead-out, correct offset with a minimum shift required
Whenever a disc is dumped with offset correction, this should be documented in comments.
And then for the rare headache cases discussed in your last post where it's impossible to shift out data from lead-out/pre-gap (data is wider than allocated TOC space for it):
3. Use 0 offset and preserve relevant non-zero data in separate pregap.bin or leadout.bin. I don't see any advantage in trying to include this data with the main dump through a custom cuesheet format or whatever, but if it's decided otherwise, that's fine by me.
And for the DC / PSX or other discs that have missing relevant TOC / pre-gap / lead-out data, we should also preserve this data in separate files (offset corrected if possible).
As for offset matching and "universal" checksums: Audio checksum databases like AccurateRip and CUETools are already ignoring leading and trailing zero bytes, so they are essentially already storing "universal" checksums? I think this is beyond the scope of the Redump project and would require too much work and too many changes.
Guess we still need to figure out how add the separate files in the database, with iR0b0t not around. Maybe resort to storing .dat or checksums in comments for now, similar to Xbox PFI/DMI/SS.