Do consider changing the terminology in the rules to need a "movie file" and not an "input file". All of the emulators call them movie files. Perhaps go on to clarify that a "movie file" is produced by the emulator itself, and that it merely records what inputs you pressed on what frame and is not an actual video file.
I am bewildered by the claims that this could affect performance, it really shouldn't. The mod team needs to add a very detailed guide on how to record movie files on each of these emulators because one has to be doing something very wrong if this affects your framerate in any way.
BTW the avi file from nestopia is not what they are referring to with "input file" Tecate, as you said, that would be redundant, they mean the nsv file. A more detailed guide is essential to dispel this kind of confusion.
While option 1 might be tempting, it could add to some confusion for newcomers. And I really don't think we need a centralized highscores website, this is just going halfway on what we really need: a centralized gaming records website. How about buying a whole new domain (gamerecords, gamingrecords, gameleaderboards or whatever is available) and redirect both speedrun.com and highscore.com (if it can be eventually purchased) there.