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Layout of tabix based features is inconsistent due to assignment of IDs #1244
Yeah, it seems like the file offset isn't going to work for a unique ID. I think it's because (and I could be wrong here) the file offset is calculated not from the beginning of the file but from the beginning of a block. But since adjacent blocks are merged before decompressing, the offset might be different depending on whether prior blocks were merged or not.
I looked and I think GFF3Tabix is the only thing using the file offset now, so hopefully that's the only thing we have to fix. Maybe once I figure out what to do with VCFTabix I'll do the same here.