Its probably way too expensive to render the megatexture dynamically like that, I think thats the reason they bake the bumpmap onto the diffuse, im pretty sure they're doing the same with idtech5 for the same reason.
wow.. I am glad that actually someone replied at all...
Now if this turns out to be the case for idtech 5, that would be quite a shocker for me

I can confirm for now that there seems to be no way to blend in another bumpmap pass to a megatextured surface for etqw....
last I remember, the only reason there's no bump mapping in ET:QW was because it didn't look good, so it was baked. But you can still do terrain as a normal texture if you wanted.
I thought the only problem in Quake Wars was the interaction shader? You might also want to look into the process of compiling a MegaTexture...I recall there were different settings as far as lighting and quality where you didn't have to merge as much stuff in (though I'm not sure that goes as far as having a separate bump map).
As far as id Tech 5...for Rage, they're baking the outdoor lighting to speed things up significantly, but they can do it in real-time as well. In fact when they're developing the levels, it is real-time...for the final version they compile a bunch of stuff down, but it's all controllable so it can stay real-time if they choose that.
Can't remember how I know this, but initially etqw megatextures had a normal pass. This may or may not be visible in the first trailer (in the beginning where you see the badger driving down the moonlit road casting shadows with its headlights.)
It may be possible to modify the megatexture shaders to get this pass back, but it's way over my head.