I've just done this, and HMRC in the UK are really quite sensible about this situation IMHO.
Their tests of self-employment attempt to look through to the economic reality of the situation, and the reality of a first freelance job is that you'll tend be working for a single organisation until your business develops. If that's still all you've done after a year or so, well they might start to beef.
I got a letter from the flight school that was going to give me work and put that in with my VAT registration, and by the time my first return came round, I had a few invoices to put in (albeit not for much money !). Since I'd blitzed out the CPL and Instructor courses within the six months before registration I was able to claim back the VAT on all of that, plus the small VAT element on the books for the ATPL groundschool which was within the three years cutoff. Came to just over £3,000.
Very nice thank you !