It's a matter of choice but for information my Td4 has just passed its MOT for the 3rd year running with a bypass fitted. It's a "stealth" version but there are so many F1 Td4s in North Devon that it's impossible that the tester doesn't know what an EGR bypass looks like. He also commented that the emissions are "silly clean". My assumption is that either the bypass is considered passable or that testers have personal leeway.
So, just done some reading, instead of contributing more nonsense to the forum . It seems that a blanked or entirely missing EGR system will not cause you to fail an MOT. You will fail if the emissions fall below the threshold as a result of the inop EGR. However, a missing or obviously modified DPF will fail your MOT. I thinks that where I was getting mixed up.
Out of interest, have you made any intentional changes to your TD4 that give you "silly clean" emissions?