I've heard 'fair not equal' used on both sides of the gender argument.
Transallies have used it to me with the meaning 'okay, transwomen aren't women, they're not entirely to be considered equal (ie the same) as women, but we need to be fair and include them.'
I've heard GC feminists use it to argue against, say, Laurel Hubbard in the sense that 'we're demanding fairness and requiring us to treat LH as a woman (our equal) is not fair.'
Is this a deliberate tactic to sow confusion? I'm very wary of the phrase now and always try to pick it up by asking the person who's used it to clarify what they mean.