Its quite simple, the NBU gets proportionate funding from the EU for the number of colonies that are registered in the UK. Currently this allows them to implement the healthy bees plan and employ about 50 seasonal bee inspectors with an aim to try and help us beekeepers by inspections and education to keep the UK bee populations healthy, whatever their origin.
Less colonies registered = less bee inspectors, due to available funding.
The bee inspectors really don't mind what bees you have, although they would prefer them to be friendly, they just want to ensure they are healthy and remain that way.
Yes they might be directed by policy decisions, which may or may not make sense, but they are not bee police and no one is ever in trouble for keeping the wrong bees.
They are well trained, operate to ISO 18001 standards and are the envy of the world when it comes to honey bee inspectorate. Registering your colony numbers just helps them justify there job in a world of ever increasing cut backs in public spending. Oh and the service they provide costs nothing at point of use, yes it comes from tax payers but so does a lot of other things.