<<You would need to pay for one ticket from CDG to Lyon, and another from Lyon to Dijon>>
No. It's easy as pie to reserve the whole voyage in one fell swoop. You will end up with two ticket segments, but it's not rocket science.
And changing trains in Lyon isn't a headache, either, no more so than changing trains anywhere in France. You always have to push your way through people to get to your next platform. You're making this out to sound way more difficult than it is.
And the Air France shuttle is no longer called Les Cars Air France, hasn't been for a year or two. They are now Le Bus Direct. Sounds like your information is out of date.