'fraid there aren't any universally "right" answers to most of your questions. Partly because there are so many different colors, some of which stack well and others of which are best reserved for highlights or "spot color". And of course it is dependent on genre and creative intent as well as on the specific timbre of the instruments and voices, the performance and the room acoustics.
So a colored pre may be an advantage or a disadvantage, depending on all these factors. For example, lots of folk like 1073 pres for vocals, which undoubtedly impart color, but they do so in a way that retains clarity and enhances forwardness and depth/thickness. Some other colored pres are generally less well received on vocals.
The use of a single pre for all tracks on a recording is the traditional (particularly console-based) approach, with the use of a mix of flavors being a more prevalent in the past decade or so. But both schools of thought are alive and well.
There are some colored pres that typically stack very well indeed. Others less so. It is very much a matter of opinion and taste (and it's *your* taste that matters when it comes to your own projects!).
Cleaner pres tend to add less thickness or additional harmonic content, and tend not to emphasize particular frequencies. While that is generally better for accuracy, it may (or may not) give you what you would consider to be the most subjectively pleasing result.
Personally, I like choices and have a mix of colored (Neve, API, Aurora etc) and clean (Crane Song, Avalon, AEA etc) on hand. It works for me - but YMMV.
