Valid point; I wonder if any research has been done on this?
I'm not aware of any that has been done with regard to rail vehicles, but there was a (well-reported at the time) piece of research by a company called CNW into cars which looked at the 'dust-to-dust' whole-life 'environmental cost' of various different models.
It made headlines at the time because, under its terms of reference, the Jeep Wrangler came out as the most 'environmently-friendly' car that was researched, with the Toyota Prius in 74th place, behind the Aston Martin DB9 and BMW X5. I can't find the original report online at the moment, but Googling brings up a number of the press articles that it generated.
The thing about research, of course, is that someone has to pay for it and, generally, that's someone who wants the research to conclude that their position is justifiable.
The snag with the UK rail industry is that, as you mentioned above with regard to your own car, on a pure grammes per passenger km basis, a new Volkswagen Golf Bluemotion carrying four passengers emits less CO2 in gppkm terms (32.5gppkm) than even a fully-loaded Voyager, which is calculated (from what I can see) at 37gppkm.
That is, of course, a bit of an inconvenient truth when it comes to positioning rail as 'green'.
If you're narrowly trying to promote the notion that the 'dust-to-dust' environmental cost of rail vehicles is lower than road vehicles, the other risk is that it walks fast and backwards into the extremely successful marketing position for road vehicles, which is always a combination of newer, quicker, cheaper, smoother, quieter, safer, more private, more comfortable etc.
Even if Voyagers and running under the wires were banned overnight, trying to adopt a rail marketing strategy based on actually promoting older standards would be brave, I suspect, and you'd struggle to drive modal shift from roads to rail if the marketing angle was to promote HSTs over new 800s (see, I knew I could get this back on topic).
Going OT again, though, it's one of the reasons that I think that a chunk of the Railcard strategy is misguided if you're rationally looking at decarbonising transport, but that's maybe for another place.