As a future professional pilot this should be well within your capabilities to research and understand the regulation - this is a basic skill of any pilot. Also given the large amount of money you have no doubt parted with, this is really part of your due individual due diligence to understand.
Without giving you the answer directly however.
The Competent Authority (as you call it National Aviation Authority) that you should be talking to is that which holds your medical records. It does not matter if you live in Spain but have a British medical - the state of licence issue is the one you need to talk to. So first of all speak to them only.
This is because although Part FCL and the AMC to Part FCL has the regulations, CAs are allowed to issue Alternative means of Compliance (AltMoC) which may only be applicable to the licences/medicals they issue.
Then you have the complexity that you may be training at an ATO regulated by a different CA. That ATO must comply with their Operations and Training manuals, which may include national AltMoCs. If their training manual says that you have a maximum of 3 years to complete the course and you didn't then you are stuck regardless.
Appendix 3 of Part FCL Section A covers ATPL integrated courses. Section B covers CPL integrated course.
The AMC to Part FCL has requirements for Section A and B including
The ATP integrated course should last between 12 and 36 months. This period may be extended where additional flying training or ground instruction is provided by the ATO.
FCL.025 c) 1) ii) does state the ATPLs theory exams are only valid for 36 months for the issue of a CPL or IR.
So given the above it seems fairly obvious you have to do the ATPL exams again. It is irrelevant to ask why, because that is the law, and there are limits set to try and catch a global spectrum - not on a one on one basis. If laws were one on one - my speed limit whilst driving would be 100mph
In terms of what your flight instructors were and were not allowed to do weather wise - it will have all been in your Operations Manual - a document you should have be intimately familiar with during all your flying. If you were completing VFR training their reasons sound legitimate.