I assume you're asking in reference to the guy on RHDN who using a .SFC file?
I didn't wanna say anything about it there because he seemed like a nice enough guy and it would only complicate the matter, but I'm extremely surprised it even worked on a .SFC file.
Technically, you can use whatever base ROM you want, but I don't think FF4kster will even open the file if it's not in .smc format. It will be able to load a 1.0 ROM, but I can tell you from experience that not everything will edit properly.
Moreover, you're very clear in the "ROM Information" section of the Namingway Edition page about what ROM should be patched with your .IPS, so unintended results stemming from the use of the wrong file qualifies as user error and not hacker oversight.