On a TT system a N-E fault might not be detected by the RCD as you say. For example if the N is only a 2-3V above E and your rod is, say, above 30 ohms then it is going to be doubtful if a 100mA S-type RCD would see enough to trip.I guess in the house on a TN-C-S supply if you had such a fault (say from a mouse in the loft chewing some cable (yes the mouse shouldn't be there and the cable should be protected if they are there)) then even if the RCD was not to work as you have such high earth fault currents then the MCB could work as a back up
In your case, as you have a MFT and know how to use it, it would be easy to periodically trip the main RCD (as it should be tested anyway) and do an overall insulation test N->E without having to disconnect anything (in effect you would be doing N+L to E as there are bound to be loads L-N even if you do the decent thing and pop each MCB before the main one)
At least with T&E a mouse-nibbled cable is likely to leak L-E and show up quickly to you by the RCD tripping before you get to the high faults currents that L-N would see before the MCB trips. Not as quickly as it will to the mouse though...
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Of course if any electronics are still plugged in (as it might be if you are just doing a RCD check when clocks change or whatever) then testing at 250V would be sensible.
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