Creating new empires is fine as long as they are not "wink, nudge" copies of other ST series/movies empires: no Gorgs with cube ships, no Fardassians, etc. In fact, one of the fan-created empires will be seeing print in module E3: the Borak. The Peladine were also fan created. They do stand a better chance of seeing print if they are not totally web-published as people get unhappy about paying for something that was free.
House rules that don't go off into forbidden territory shouldn't threaten our license. If you don't like the way something plays, then suggesting a house rule shouldn't affect anything (as long as Mongoose doesn't care). However, it has been our experience that house rules may be compensating for local play styles and would be unbalancing if another play group adopted them.

Adopt house rules at your own risk and it voids the warranty if the game breaks for you.
Do we care if you paint up FASA or other legally acquired models? Nope. Do we care if you kitbash one of our models, stat it up for TNG,
and post it here? Yes. You're fine until "post it here." I cannot tell you it is fine to post it anywhere on the web. That would count as encouragement of breaking our license. I can tell you that we have far more pressing things to do (such as designing games) than surf the web. If it is reported to us, we would of course take action.
Does that help clarify things?
I hate to sound so negative, but it is what we have to do to keep the license we have which keeps us in business.