So the question stays - have you seen these 3 variations and do you know when/for what each is used?
I have never seen any other version than the first one.
BUT I have an answer for you, which might be just right (disclaimer: I don't know it, I just use my commonsense/thoughts)
Tileset 1 is the normal version used for dialogue. We all agree on that.
I suppose Tileset 2 and 3 were never made for dialogue - but for the main menu! Let me elaborate:
Tileset 2 is not a "slightly darker version" imho. Look closely - it's a black and white version. It was probably created to display a petrified character.
And Tileset 3 was most likely created to display a KO/dead character.
I am pretty sure because a b/w tileset and an invert tileset were both actually used on FFIV Advance to distinguish petrified and dead characters on the main menu respectively. Since the remake style of the 3 Advance releases (IV, V and VI) are very similar (window color, font, title screen, bestiary/music player, post-game content...), I think it's not far-fetched to say that "petrified" and "dead" menu portrait tilesets were prepared for FFV Advance as well, after being used for FFIV Advance.
While being appropriate for the FFIV menu, it got dummied out for FFV. I suppose the developers dicided to stick with the sprites since it's much faster recognizing which job the characters are using. If the portraits were used on the main menu, you would have to read out the jobs - which wouldn't be too bad, but still imho taking more time than recognizing 4 job sprites within a single blink of your eye.