The 5mm hole is a good idea, & i have heard from a ford lady that it works well, but better still ask a company called Allisport for advice , they make an EGR defeating device specifically for the TD4 2.4 Defender 90 that you have, it looks like a trumpet which installs at the end of the EGR outlet, rather than a "gasket with no hole " that you probably have fitted so may address your issues. As to whether all egr blanking plates needs a hole in, it varies between vehicles, it may work OK but may not , try it & see...
PS - i dont blame you for wanting to avoid the "warranty", my customer in Essex that has had his TD4 Defender 90 remapped has had the same rubbish , time wasting , "warranty support" that many ford van owners on here have experienced.
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www.vantuner.com for egr deletes - power tuning- tricky limiters - cruise activations - key programming - updates & recalibration.