garageCube

Can Madmapper change the color of a fixture on tempo without changing the scene? In other words, without using auto-play.

If not, then can it turn the luminosity on/off on tempo?

You can create a cue that will modify Red, Green and Blue value of the selected fixture, with fading.

You can create a "Cue Scheduler" module that will trigger each N seconds the cues on row N from column N to column N. This will not trigger scenes or change current column. It will just trigger the cues.
In MadMapper 4.0 you can have multiple cue banks and Cue Scheduler can target a chosen bank. So you can have a bank with cues for changing all parameters except colors (donnot use Scenes in this case since it stores everything), and a bank with just you color changes.
You can also create multiple "Cue Scheduler" modules that will trigger different cues with different settings.