Thanks for the feedback. Can you upload one of these roms so I can check it?
There is still an encrypted ROM from my gold edition in this previous thread: viewtopic.php?f=9&t=2101
It uses the script you added in that thread(sega_classics_gold.bms). The produced file was titled correctly regardless of which version of QuickBMS I used. If an older version of QuickBMS is used(I used .75) it should produce a use-able ROM. If the script is run in .90 it should create a ROM that is 3 bytes more(and they should be the bytes I posted above, at least that's what every ROM had added to it for me.) If I deleted the first 3 bytes of the .90 ROM with a hex editor it ended up the same as the ROM created with the older version.
From my testing, a ROM extracted from a Steam version .pak with the "sega_classics.bms" script was the same as a ROM extracted from a Gold edition .pak with the gold script(provided both paks were the same underlying game). This was the case as long as the same version of QuickBMS was used(I.E. the game extracted from .90 would be the same whether Steam or Gold edition(including the 3 extra bytes), and if .75 was used the steam and Gold would be the same as well).