Well, to throw a wrench into this conversation...
When one understands in the theory behind how filters work, it's easy to see that there are many variables that will affect the "factor," which is basically there to prevent underexposure. As michael_r points out, erring on the side of overexposure when one recognizes a situation that may deviate from the average and require a different factor is good insurance against underexposure and won't change the effect of the filter (as long as densities don't block up on the film's shoulder).
But, as Sirius points out, applying a filter factor does not give you "control" over how different colors are rendered; it is the filter's characteristics that determine that.
The main problem with just applying filter factors, as I see it, is that one also has no good way to visualize how the different colors in a scene will be rendered relative to each other. Sure, we can expect that objects the same color as the filter will be rendered proportionally lighter than without the filter and vice-versa, but that isn't nearly precise enough to figure out how much separation there will be between different colors, density-wise, in the negative or final print.
One situation I'm confronted with often is that of green trees against a blue sky. I read the trees with my meter and the sky. My meter reading, without any filter, says that the sky is one stop brighter than the trees. But I want the opposite - darker sky and lighter foliage - so I reach for the green filter. But will it do the job? No way to really know if you just apply the factor and make the exposure. It's a crap shoot.
So, I do my best to quantify the filter effect by taking meter readings through the filter. Yes, I know that there are a plethora of variables that can make my readings inaccurate, however, it is the only way I know to get even an approximate idea of how the filter will affect colors in the scene. And, with some experience and a few tests, one can eliminate many of the variables that affect the meter reading through the filter.
I'm pretty confident when I read through the filters I use most that I can extrapolate to within less than a Zone how colors in the scene will be rendered. I know, for instance, that reading through a red #25 filter reduces my meter's response by about a stop, so I add that mentally. With a green #11 filter, my meter reads just fine, same with yellow #8 and #12 filters. The green #58 filter requires a bit of fudging, but it's closer than the #25. Etc.
So, back to my scenario: I get out my #11 filter, take a reading of that blue sky and the green foliage and find that, whoops, they both now read the same. I've darkened the blue sky and lightened the foliage with the filter just enough to create a tonal merger, which I don't want at all. So, I try other filters and combinations. Often, I'll end up adding a polarizer to the mix to darken the sky a bit more to get the effect I wanted. Or, I'll use a stronger filter, or I'll re-imagine the scene, or I'll give up and not make the shot at all.
If I had just applied the filter factor, I would have wasted a sheet of film...
Best,
Doremus