Well...honestly, that doesn't sound like what I understand to be affiliation, or what generally defines affiliation between RP boards. Affiliation is when one board, or RP group allows another board or RP group to advertise on it, like setting up a partnership. The RP groups/boards do not necessarily have to be of the same type (e.g. HUE, a Hetalia board could affiliate with a Naruto RP board, etc.) but generally same anime/themed boards like to advertise/affiliate with each other in order to gain more members/mutually interested people.
Starting your own AU outside of this board would, if agreed upon by the admins, count as affiliation if you were to advertise/we were to advertise on your board. We have not yet decided whether we will open up such advertising (as it has caused problems in the past in other places, not necessarily here on the board, and we are unsure whether we want to do it ourselves yet), and if we do we have not yet decided whether we will leave affiliation exclusive to Hetalia-RP boards, or whether we will open it up to a wider range. If the former is the case, you would not be able to affiliate unless your RP board was a crossover board. If the latter becomes the case, then you would, with permission from the admins (since our idea of affiliation is mutual advertising, since we are not an advertisement community)
If you wanted to start a Star Trek AU WITHIN the board (since our goal is to create multiple AUs here XD), then you would first go to the Forum Discussions board to suggest your idea to see if there would be interest. I do know already that someone already requested a Star Trek AU, and that particular AU was added to the poll for the new AU for the board (but was voted out one of the rounds).
If you still wish to RP Star Trek on HUE, but do not want to wait for the new AU, you are also welcome to take AU ideas to the 'Non-Themed' board. This board has various sub-divisions, so choose the one most appropriate for your AU. These rules are outlined in the descriptions of the boards in the Non-Themed board, with each one having its own set of rules (that aren't that different from the regular old rules anyway XD). Others have taken their ideas and started RPs within the Non-Themed board, so you are free to do that as well.
I hope this helps. If you have further questions about setting up your own AU, feel free to contact me via PM. If you wish to see if anyone else would be interested in your AU, feel free to post in the already started thread about a potential Star Trek AU with those interested, and set up something in the Non-Themed (which is defined here as 'something people are interested in that doesn't have an AU yet')