Good question, some games stored this data on nvram, and in that case all versions of MAME will save the data to disk in the nvram folder. Some of the .hi files generated from the hiscore.dat actually do store this type of data. A good example is bubble bobble, the game decides which bonus items to give based on how many of other bonus items have been given. Without the patch, these values are always reset on exiting MAME, making for pretty predictable items. With the patch, it's much more similar to an arcade machine that's been on for hours, and been through multiple plays.
I haven't looked at street fighter alpha 3 in the hiscore.dat yet, but if it doesn't include those bytes, someone dedicated enough may go through and look for these values in memory and add it. Once/If the values are in the hiscore.dat it's a simple matter of opening up the sfa3.hi file and modifying those bytes in a hex editor. It's also possible this data is stored in nvram, and if so, nothing would need to be done in the hiscore.dat, and you would modify the sfa3.nv file. This can be tricky, and it's not always simple as changing a 00 to 30. Some games have internal data protection with checksums, or requiring the data to be in multiple places (see Robotron scores in nvram for example).