You could spend the night in Torino if you go through Italy. Or Aosta, a smaller town with some good Roman ruins.
Regarding Chamonix - Geneva - Beaune, I am not 100% sure you need to visit Geneva. It is a pretty city, do not get me wrong, but I find it a bit grey, and driving and parking there is not very convenient. You would need to be careful not to use any motorway in Switzerland as it requires the purchase of a ~40€ toll sticker.
I would much rather recommend Annecy instead. Chamonix - Annecy by the A40-A410 (other routes are much slower), park at the Courier garage.
Then Annecy-Beaune by the D1508 to the A40 (motorway, but beautiful in the first stretch), then on to the A6 for Beaune.
If you do end up visiting Geneva: you could decide to cross the Jura mountains on your way to Beaune. I have never driven the whole route, but parts of the D1005/N5 (which goes Gex-Champagnole-Poligny) are beautiful, and you end up on the A39 motorway near Poligny. If you only have one night in Beaune, do not do this, but if you have more time, why not. And do not do this from Annecy either, the detour is too long.