More mass definitely adds up. Take a vintage les paul for instance, you've got a lightweight trussrod, lightweight tuners, and a lightweight bridge (aluminum). I think this all adds up to impact the tone in a way that one can hear. Now, replace these things one at a time and listen, and the differences will probably be subtle (with the bridge probably being the most notable tonal change), but they will all add up. We're talking a vintage les paul here and not a squier bullet.
I personally prefer to stick to the vintage formula as much as possible, but I highly doubt that all things being equal that going to a double exanding truss rod will impact the tone of the instrument in a negative way.
I've never built a guitar neck from scratch, but I'm seriously thinking about going with a Hot Rod for my first couple of necks until I get the hang of it. Using a single action truss rod and having to route that curved channel seems like a little too much for a beginner to deal with.
Also, Gibson's 50's explorers and v's are made out of all Korina and use single action truss rods. I've never heard of them having ANY neck problems.