Having skimmed the whole manual and using the knowledge I have, I think that where possible, by far the best solution will be to "restore" your chassis/monocoque back to stock and use as many total stock parts elsewhere as is required to get your points count well up BEFORE this becomes a big issue and you get caught - avoiding BIVA like the plague is surely the best solution - getting caught could be as simple as presenting for an MOT in the near future, the facts are that these rules have been around for years, we just don't know how quickly or how harsh the crackdown will be!
Surely it's better to have a vehicle that rides a bit higher and is a bit more stock that you get to keep on the road, rather than get pulled and suddenly find that you have a very expensive pile of scrap...
I do agree that the reg's as they stand are to some (minor) extent still open to interpretation, and I think that while this gets nailed down with clarification we're going to see some very expensive test cases where owners will lose a lot of money - the rules have been there for over a decade, responsibility will rest on the shoulders of the owners and I can't see anyone taking VOSA on to argue the toss as I'd bet my left buttock that the ban and seizure of the V5C will come first and quickly and you will then have to prove your case or comply with BIVA to get a new ID...
My personal belief is that you won't get the chance to restore after you get a ban - I've not read around the subject extensively yet but what I have read hints that the V5C gets seized and that's it, no way back without going forward through BIVA to get a new ID - I think a lot of people could be losing a lot of money and the wider modifying scene, whatever cars you're into, will be losing a lot of cars before this is finally played out.