Yes our printers have full nozzle temp control. The fan has nothing to do with the nozzle temp. Accurate PID tuning of the nozzle temp will yield a perfect flat line temp. The nozzle fan is used to do many things.
On very small prints it is used to cool the layers just enough that the print doesn't deform before the next layer goes down.
It is used with great results for bridging as it will cool the filament just enough to allow it to stretch tight.
It also helps greatly with steep overhangs that would normally require support.
Your theory of a nozzle fan messing up layer adhesion is not true. Think about a large print, by the time the nozzle gets back to a particular location for the next layer, the previous layer most certainly isn't still at or beyond the transition point.
You always are printing on a layer of cooler plastic so no worries about that.
My advice is, if you've never experienced a good G-code controlled nozzle fan, try it!
Printit Industries Model 8.10 fully enclosed CoreXY, Chamber heat
3-SD3's & a Workbench all fully enclosed, RH-Slic3r Win7pro, E3D V6, Volcano & Cyclops Hot End
SSR/500W AC Heated Glass Bed, Linear bearings on SS rods. Direct Drive Y-axis, BulldogXL
Thanks to all for your contributions