Thats not quite how Noesis plugins work, you just place the plugin in the python folder and start up the program. You don't need to select or enable it, as its automatic.
Chroxx script reads .bcres files not .bmd if I remember correctly, but you cant just rename a .fs file to .bcres and expect it to work, it could work (works somewhat in EFE) because of the way the script reads the format, it it see's its not a single file and actually an archive then it may decide it can't do it, theres no hard and fast rule with such formats honestly.
But index.fs is only the index anyway, that doesn't actually contain any models at all, it simply has pointers to the offset locations in the other .fs file, that other file is what you want to be opening.
However instead of wasting your time using the .fs files, just use quickbms to extract them and then they'll shoot out a bunch of .bcres files, then you could simply try opening those in Noesis instead, some are still screwed, others are fine and some dont open at all, its largely because Bravely default seems to change its format ever so slightly a few times. The models used for AR don't wokr the same way as the models for ingame at all, same format but most of the body is missing in all software.
Also that link, is simply for downloading Noesis, not for getting the plugin itself.