The CAA published a Skywise notification regarding this topic, [
link]. There are still different privileges, but the difference isn't as pronounced as it was.
You can use your national licence to fly Part 21 and non-Part 21 aircraft. If this licence has an SEP class rating, you're restricted to the privileges of a LAPL (ie. No IMC/IR(R), 2000kg weight limit etc).
There are no such limits on your UK FCL PPL with SEP class rating. This licence is also valid for Part 21 and non-Part 21 aircraft.
Your instructor/examiner could have signed the national licence. The hours apply to both licences. Further details and exceptions regarding microlights are published
here.