I noticed on Heritage that no matter if a Runic Atlas is Exceptional or not it spawns with 100 charges.
On OSI, if a Runic Atlas spawns without Exceptional it is 80 charges.
If it spawns with Exceptional it can be 80, 90 or 100 charges.

I'd say you can leave Exceptional always being at 100 charges if you want, but non exceptional should not be more than 80 charges, otherwise being exceptional has no benefit at all.
On OSI, if a Runic Atlas spawns without Exceptional it is 80 charges.
If it spawns with Exceptional it can be 80, 90 or 100 charges.

I'd say you can leave Exceptional always being at 100 charges if you want, but non exceptional should not be more than 80 charges, otherwise being exceptional has no benefit at all.