I've read through the Vehicle Lighting Regulations a few times and I still believe the following is correct.
You CAN switch your spotlights (or any other additional front facing main beam lights) on manually or on with the main beam. In both cases your normal headlights must be switched on and in both cases you must have a warning light to show your main beam / spots are on. It's not compulsory to have them ONLY switch with your main beam.
You CANNOT however have spotlights (or any other additional front facing main beam lights) switched on, on their own. They must be incorporated in the headlights ON circuit.
Headlamps, dipped-beam, main-beam, sidelights & fog lights i.e white forward facing lights, must be working for the MOT. Anything else i.e spots, flood lights are NOT included in the MOT testing procedure and therefore do not need to be in working order (like removing the fuse)
As to the legallity of having the "facility" to switch spots on on their own is open to debate, but surely thats what the RTA is trying to enforce. Being caught on a public highway with them actually switched on, on their own is definately illegal.
Thanks Budgie for your reassurance over the fuses. The headlight circuits are already protected by 10a fuses, I just wanted to make sure I didn't need a bit of overkill !