We're going to go with "not meant to be the final sound reproduction device" for whether or not something's a stompbox. So no, amps aren't a stompbox. Also I think most rack gear is outside this definition unless it's got remote switching.
A contestant wouldn't be penalized for having a preamp or amp component as part of a stompbox effect.
For example, if someone entered a tubescreamer/noisy cricket combo in one box, we wouldn't add or subtract points for the noisy cricket. If they entered a noisy cricket in an enclosure without any effects, we would have to disqualify it.
I think everyone here knows what a 'stompbox' looks like, and if you think what you're making might require judge approval, you can ask in private.
Besides, if you make an amp as your entry, how the heck would you give an example of the uneffected setting through the device? Plug your guitar right into the speaker? :p