Until exit takes effect (two years from starting the article 50 process) the UK is still in the EU and the law doesn't change. Maybe the law doesn't change even after that – nothing is certain yet.
You are right, EU law applies but it can be circumvented, for operators and therefore FTLs, under the flexibility provisions of article 14 of the basic regulation. Now that the European parliament have stated their position and would also, subsequently, require the remaining 27 states to agree re entry for the UK, there is no way that the agency, the commission or the EU courts would formally entertain addressing any deviation or punitive action. By the time any deviation from a UK operator could be addressed by a UK court or the CAA legal enforcement department, it would be unreasonable to uphold a conviction under a diminishing and time limited rule.
So, during this transition period, the argument for sticking or busting the rules may come down to risk v reward for the operator. Any brief worth their fee could easily argue against the EU rules being restrictive, anti-competetive, unsafe etc. as long as reasonable steps were taken not to undermine reasonable standards such as national or icao types.
As I see it this is a tricky period, the transition, as a well funded operator could justify the expenditure required to work around previously imposed commission obstacles.
Take a scenario like grounding an aircraft designed in britain with a EASA type certificate using an EAD issued by EASA. In law, would it be unreasonable to continue to operate the type if it could demonstrate it continued to satisfy UK type design standards? Is it not highly likely that the operator of this type might bring a claim against, say, the UK CAA if their fleet was grounded, as there was no basis for appeal against the EASA decision using the EU legal system?
In 2 years time we will see how creative the stakeholders in UK commercial aviation have been. When parliament starts this exit process, I dont think operating or complying will be as clearcut and rigid as some think.