I think we are all getting a tad exited by this regulation, the problem with the BS7671 is it tries to stay concise 'believe it or not' while covering the range of domestic to industrial, the issue here is that you will never see any concerning issues domestic wise unless we are talking a large property with a hefty supply, as it goes anyhing 1ph and less than 100amps isn't ever going to see a notible/worrying effect from eddie currents if cables enter a metal enclosure through different holes (Unless they are metal sheathed).
With regards to the earth running through the same hole, well again this is a simplification of a more complex issue, if your Line(s) and if applicable Neutral are encased seperately in a non ferrous metal like individual steel conduits or singles SWA'a then this exagerates the effect hence the point made earlier about singles SWA not been permitted, earths been part of the collective is relatively new (explained later).
When you go 3ph and/or heavier loads than your average domestic is when this issue see's reality, I've seen loads of domestic breaches of sending L & N through seperate holes with no issue at all but simply because its not an issue that's not to say that the regulation should be ignored, yet I have seen banks of lighting over 3phase run to a M/C switch bank through seperate steel conduits where the total loading was only approx' 20amps per phase and the conduits couldn't be touched as they was that hot due to eddie's. Going back to the earth from an earlier comment, fault currents are not the reason why the relative earth for said circuit or supply earth run through the same hole, a correctly designed install would see a high fault current for a very brief period and no where near the time required to create any real issue with eddie currents, the reason is down to progressive trends of having more electronics and equipment producing harmonics or designed earth leakage leading to earth currents but again no issue at domestic level. It's designed to teach you to apply the regs on all occasions regardless as this hits home more and also covers problem of describing exactly when you need to apply the reg' and the complex calc's needed to do so....
So yes L/N/E needs to enter through the same hole to meet regulation, is it required is a different matter but its hard to calculate as too many variants can effect the outcome and the eddie current produced.
