Homonculus,
The way I've had the VAT situation explained to me is that the company will be more like 'Red letterdays' they sell flight vouchers and they wont need CPL's If the tax man asks "why am I claiming flight training" I explain that I'm going from PPL to CPL to FI which is employee (Me) training.
so I go from selling vouchers and passing the customer over to a qualified pilot to carry out the flight.
when I am qualified I could carry out the voucher flights, as a lot of pilots are self employed and charge out there service's that's what I will do but I charge VAT to the company who are employing me.
As the chances of getting a full time job as a pilot with a fresh FI are pretty low, the work most likely would be contract work which is where the company / I will be earning money as a pilot