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What's the purpose of minimum and maximum fan speed? I'm not seeing any variation during prints, except for bridging fan speed. Near the end of my prints, the tip of the part is very small, and heat builds up, getting very mushy. If I am watching, I'll reduce my nozzle temp and turn on fans to max. I would like the fans to come on when the minimum layer time is hit, causing the print to slow down.
I also want to add that I don't want the fans on within several inches of the hot plate, because the plate can't keep up, and the printer eventually aborts. Since not all parts are the same height, setting a number of layers to suppress the fan is not really what I'm looking for. I also switch nozzles, so layer height vs number of layers is not a constant.

If you're talking about Slic3r, the fan speed settings work with the other cooling settings. Not sure how many of these make it into the MatterControl interface, but they're all there if you download from slic3r.org:

The full fan logic for parts of the print that are neither first X layers nor bridges only works if you have auto cooling enabled and your "enable fan" layer time is longer than your "slow down" layer time. The "enable fan" layer time is where the minimum speed will be used. The "slow down" layer time (and shorter) is where the maximum speed will be used. Between those layer times, linear interpolation is done.

Not sure if the 1.3 branch will change it, but for the moment, off for first X layers is what's available for that functionality.

The only thing that really works for pointy part tips (regardless of slicer) is to print a second copy or a sacrificial cylinder/arbitrary part the same height as your part. As the layer profile gets infinitely small, so does the layer time, and even if you're using fan it has a real uphill battle.