In my life before flying, I was a musician doing the same show every day for the same producer (for years). All theatre musicians are paid on a self-employed basis using BACS by the same producer on a weekly basis. The musician is responsible for paying their own tax liability at the end of the year. I can't see why flying should be different. In theatre, a "fixer" is the orchestral contractor, but they aren't allowed to hold any funds, other than their own commission.
I wonder if accountants are aware of this and if it's worth arguing the toss?
Applemacster