I've tried running Game Converter from a different folder from the game directory, if that's what you mean. I've also ran the Converter from the game directory for that matter.
I install my Square store version to D:\FINAL FANTASY VII. Then I run the Converter, it recognizes my game install location as D:\FINAL FANTASY VII, I select E when prompted what language, and the patcher does its thing without issues. After this I run the Reunion installer, point it to D:\FINAL FANTASY VII, and upon pressing Next it warns me my ff_en.exe is the wrong size.