OK, sad but true - I spoke to a mate who is a bit of an oracle about this sort of thing last night, to get some clarification.
His interpretation is that you can alter away from the homologated cage you've started with, provided the homologated design meets the minimum specification for tubing etc laid out in the Blue Book.
Because a specific design has been held up to FIA/MSA requirements in terms of strength and design, it's possible that they've used under-sized, or otherwise out-of-spec tubing in the construction of the cage. Because it's been homologated this is immaterial - the manufacturer has demonstrated that due to their design the cage has sufficient strength for its application.
So provided the original cage uses tubing that meets the minimum specification laid out in the Blue Book then you can modify the cage. This would be how you could add tags to the pillars, or harness bars without trashing the ability of the cage to pass by a scrutineer.
HOWEVER if there are smaller than 'legal' diameter tubing, or tubing that is too thin-walled then mucking about with the effective design of the cage is when you're going to run into trouble.
Check the tube diameters and if they're all the same you *could* slightly dangerously assume they're all the same spec tubing and if the diameters are compliant then you can get modding to suit your requirements.
The motorway bridge is only required depending upon this assessment.