Just using the one with [!] should be enough. In any case, when you load it with the sfrom tool it should be obvious if it recognizes it correctly. Go to advanced options and see if the PresetID is changed. If it didn't, it's the wrong rom. If it did, don't change anything (don't apply any PCM patches but do apply SDA and VC patches, these should be the default settings anyway), save the sfrom and that's it.
Or... even easier to tell if the rom you selected is recognized by the database is, if the little circle in the corner is green. If grey, it's unrecognized and you would have to edit the info manually.
I don't fully understand the rest of your post. No footer is added to these roms, specially not the SMW footer. Everything that worked before will work now, what didn't work probably still won't work yet (except for these two games). I don't think you should go editing all the roms you had already inserted, there's no reason at all to do that. I think that (for now at least) you should just use the sfrom tool method for Street Fighter Alpha 2 and Star Ocean.
They should be edited to use the correct Preset ID in the footer, but thats it. Theres no reason to use traditional .sfroms created with my tool except for SDD1 games. For other games... either version of the .sfrom is probably fine for now. The only difference is you have to manualy add/edit footers for switch sfrom versions (until I know enough about the footer format to update my tool to support them).
The switch format .sfroms are probably more versatile because of the extra params, but as those havent all be figured out yet, for the most part both .sfroms formats do basically the same thing. Supply a Preset ID, MaxInput, Volume, and Special Chip byte. MaxInput and Volume are basically unused, and the Special Chip byte is only needed for SuperFX games. So maybe theres a case for using a tradition .sfrom with Star Fox 2? But as other SuperFX games on switch have that clock speed effecting param, StarFox 2 probably should too, so it should probably be used with a switch .sfrom/footer.
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That said, now that I think about it. There is a bit in the code that might suggest that traditional SNESC .sfroms might run differently than switch .sfroms. There's a check in the code that checks param74 (The one thats always set to 0x06 except for Super Tennis which is set to 0x07). When thats set to less than 6 and not equal to 2, a big switch is processed that checks other IDs and sets some flags unique to many IDs'. If it is 2 or 6 and over, it only checks for the joe and mac 2 param and if not preset, seems to do nothing. Since a SNESC .sfrom does not supply that param, its going to be seen as 0 (less than 6 and not 2), and thus should process those flags.
What all the flags do, I dont know. But they probably exist for a reason, and that reason is most likely related to optimization/compatibility/bug fixes.
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As for the SFA2 issue with my tool. I have no idea... The PAL version I suspect I know the problem with, but just haven't got around to addressing. It a bad older patch that I forgot to update. The US version used to have a bad older patch too, but I updated that long ago so I doubt you found that.
And yes. In general, my tool expect and requires either the [!] goodsnes version of the rom, or the nointro version (which are mostly the same thing) to be recognized by the database.