Are you trying to scare potential contributors or decision makers? Vanilla map sets get made all the time. As noted, the Boom choice is chasing off vanilla people in a concrete, practical sense, and I mean users of various kinds, not just contributors. Boom people are vanilla + Boom people, and vanilla people are vanilla - Boom people, because Boom includes vanilla and not vice versa.
If the Vanilla Doom people chase off the Boom people, then Freedoom will be down to about 8 to 13 people, maybe a few more. This is a likely result that should be taken into consideration.
So, you're worried there won't even be enough people to do vanilla maps, but expect many forks of the project? Rather self-contradictory, eh? If we have so much level-making power, quit worrying that the vanilla levels won't be made. People can indeed make variants eventually, but that can be left to optional initiative, as the project is better off focusing on and putting a guarantee on being as highly useful and portable as reasonably possible, especially if it's for the public, and not something for a certain clique or niche of gamers like us PC DOOM fans. To boot, if you make vanilla levels, it's not so hard to expand them and alter them by adding features later.
If Vanilla doom is so important then we can make a Vanilla-Freedoom. We can then also have a Doom+_Freedoom, and I can get a Legacy-Freedoom.
The main reason given to use Boom, explicitly, is that some designers don't like being limited by vanilla when making maps. As noted, this is relative. Others love vanilla, and yet others will make maps in many formats. Even if there is some loss in level design contributors, we can trust there will be enough, and good ones, because the community's strongest design point is by far level production. Thirty-two (or more) good vanilla levels can easily be produced well before the sprites and sounds are done.
Another reason one can suspect people may push for Boom is to plug, promote or advocate source ports with extra features. If you add Boom stuff, the IWAD will be crippled for the game "as is," forcing users to download a more-advanced source port. Of course, this agenda has a malicious side effect; any Doom engine or port that for whatever reason leaves out Boom features, even some of them, is incompatible with Freedoom or more awkward to use with it.