Sorry about that, I think I had my files mixed up and was getting a false positive.
So looking at the header settings in that database, they did more than just set the rom to ines2. They also set 2 additional settings in the header (looking at the NES version, not VS):
NES Database:
4E 45 53 1A 02 01 00 08 00 00 00 00 02 00 00 01
ROM switched to ines 2:
4E 45 53 1A 02 01 00 08 00 00 00 00 00 00 00 00
The "08" means ines2 format. That is all that I would expect to change.
The "02" means "VS PPU Type = RP2C04-0001"
The "01" means "Default input type = Standard Controllers"
I'm not sure why the database has those changes. To me the correct thing to do is update the database to accurately reflect the actual released ROM. To me the actual ROM should be the source of truth. What do you think?