If just swapping some little roller wheels might void the warranty, the owner/individual consumer drilling out a hole has got to void the warranty!
I see some Brompton dealers are advertising a complete rack/wheel kit that upgrades to the new design, but state there's no warranty unless all the parts are installed by a professional bicycle mechanic.
I'd call your statement nonsense. It has been explained now more than once
why 3rd-party wheels on the rear frame may void your warranty
on that rear frame and why this ist acceptable. Swapping out the stock wheels with other, newer stock wheels will obviously not void your warranty. So people using an L-model w/o rack are fine anyway.
The rack never has had problems with breakages due to wheels (at least as far as I know). Brompton says the 2016-onwards wheels are not compatible with the racks built up to 2016 due to the M6 Bolt instead of M5. So if you want to be totally compliant you may use the "old" EZ wheels for the rack here - they use M5 are still available. If you want the newer wheels you can either use the original bolts and the metal bush from the old, small original wheels with the 2016-wheels and they will fit onto the rack. This should in my opinion not void your warrany.
Or you make a M6 hole from the M5 on the old rack and use the new wheels with all parts from the new set, including the bolts, but this probably
will void your warranty
on the rack. You could for sure buy a new rack but this would be total overkill if you ask me.
But: As there never has been a problem with the wheels on the rack I highly doubt that a slighly bigger hole, identical to the new rack, will create a problem.
And the new wheels got invented with model-year 2016, so almost two years ago. Newer models already have those wheels as well as the 2016 rack. The Brompton-warranty on the frame is five years, the warranty on everything else is two years. Therefor most Bromptons with the old rack either already have run out of warranty for the rack or will shortly. Therefor the question of warranty for the rack for this case is obsolete for most Brompton-owners.
Obviously the outlined modification on the rack won't affect the warranty on the frame. Using 3rd party stuff on a known weak spot like the wings of the rear frame is understandably a totally different story. People that are not able to take responsibility for their homegrown modifications better should not do modificactions in the first hand...
BTW: Brompton have in the uk stopped selling frame parts such as stems, rear frames, bushings for the seat post and for the rear frame publicly as it turned out that a relevant amount of people were not able do deal with those things properly, causing problems with the bike afterwards and therefor potentially damaging the image of the brand. Therefor in the uk these things now have to be installed by a Brompton dealer.
Here in Germany they are still freely available because the assumption is that people over here more likely know what they are doing when working on their Bromptons (and possibly because the amount of Brompton riders is far lower than in the uk).