I don't think it's a bad thing. Like them or not, they have a somewhat controversial history; a lot of people worried that their projects would fork the ecosystem, or give them too much control of it - I wouldn't be surprised if they decided that it would be better for the foundation's goal of being a community effort to not be seen as having a heavy hand in it. Some people have expressed similar concerns about Facebook and IOHK as well, just from the financial influence they might have, even though their haskell projects haven't been as close to critical infrastructure as FPComplete's have.

The FP-Complete people have had clear different goal than the rest of the community for a while.

It creates some kind of partition, but it's not very relevant. Anyway, it's not very surprising that they don't want to sit on the same committee.