Does changing the cruising speed manually within the acceptable limits for the aircraft affect maintainance ratio?
No, calculation of maintenance is based on kilometres only.
Yes it does. If you are at 99.7 a simple speed override to maximum will save you a few minutes off flight plan, frequently bringing maintenance ratio to positive 100.1 etc.
Only when those saved minutes are used to extend a maintenance window, you will see this perceived effect. The requirements for maintenance (ergo the “damage points” obtained by an aircraft during flight) are still the same.
So you’re both right
Learned something new. Thanks for framing that in a way I could really understand.