All a bit surprising. HMRC have always had rules on the boundary between being properly employed and being "self employed". Those haven't changed, what has happened is that individuals (not HMRC) have been bringing court cases. It really shows HMRC have been asleep at the switch, and in fact appear to be continuing to do so. Which is surprising because the principal beneficiary is the employer, not the individual, and the principal loser financially is HMRC through not collecting the Employer's 10% of NI contributions.
However the employer may word it in any documents or "contracts", if you fall inside their definition of employment, you are employed. One of the key tests is are you expected to be working for anybody else. In the case of aircrew, if the employer is expecting to be able to schedule you up to the legal maximum of 900 flying hours, you are not able to work for anyone else. You are employed by them. This is regardless of whether you are a limited company, have registered yourself for VAT, or whatever. You can be employed by an agency, but then all these rules come down on them.