Zero: Profiling what is actually generated, versus assuming a vanilla world, is a no-brainer. Equally, charging based on the actual age, instead of just the symbols, is also a no-brainer. Putting in some additional charges based on the symbols does, I think, make sense -- the more constraints you put into the world, the more likely there's some unintentional conflict.
First, we have some mod(s) out there that mess up the out-of-game profiling. So:
Have an option to select high-priority pre-play profiling versus low-priority during play profiling.
For the "low priority during play", give people the ability to turn its speed down. One chunk per tick may not sound like much, but for many people, 20 TPS is actually a challenge in normal play. And yes, since you are not likely to go to an age that quickly, letting mystcraft do one chunk every 5 ticks instead of every tick won't really cause mystcraft issues, but will help things work better.
Second, once you do have a profile, even if it was made in a world, instead of the pre-world, store it as the base pack's profile.
Third, have some sort of "full speed profiling" command for mystcraft, so that if you are doing something like creative mode testing, you can get that profiling done NOW!.
Fourth, support both a "pack default", and a "save specific" option -- allow some saves to have different configs and profiles. Most packs won't need this -- no server setup will need this. But some people will have different configs for different single player worlds. This one should be considered low priority / low demand / low need.
Instead of creating a new dimension wouldn't it be possible to do the baselining on the overworld and then store it? Overworld would still be influenced by these vanilla ore generation tweaks wouldn't it?
You cannot assume that the overworld matches general ages. Imagine (this is real, by the way) the idea that the overworld is poor, and people go to ages for resources.