From my understanding, it's a recommendation and not a requirement to keep rifles and bolts separate - and with things like lever actions, semi's and to a lesser extent single shot firearms you can't easily remove a part to render them inert so it's a bit of a question how effective such a rule would be.
As far as your security, I think "double layer" security of a locked "stout" cupboard followed by an internal secondary compliant gunsafe is in excess of the minimum requirements that are required for meeting the requirements of licence inspection and really it can only be considered a good thing. As you say, even if a thief was to defeat both security layers then they would still not have a complete firearm.
From a purely practical viewpoint, I think you would still be compliant storing the parts in the separate compartment and this would be a lot more convenient for you in storing things etc etc. But there is nothing wrong I can think of with what you are doing?
It used to be part of the legislation that you were not able to store Class 1 material in a dwelling house, meaning that ammo stored inside a house wasn't compliant but I've since had it pointed out that the legislation that gave power to this has not been renewed and I can't find anywhere that this is currently required in the legislation still in place. That would be possibly the only thing that might change storing ammo inside your house, but as far as I can find you are currently OK to do this...
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