Well, since my thread is referenced, I guess I'll chime in.
I'm honestly not that surprised that the fan is on all the time. That fan is specifically to "mix" the air inside the unit to cool local hot spots. Eventually that air is cooled by the large metal case, but slowly. There are a couple internal components with heat sinks that may overheat even if the ambient temperature outside the unit was low.
Why isn't it on a thermostat? Probably just one more thing go wrong, plus you'd have to do testing to figure out the fan profile (or at least when to turn it on). I've built systems where we only needed the fans at high ambient temp, but we ran them all the time because it made the system simpler.
Yes, the fan will fail -- it is cheapo made-in-China. Circupool did sent me a replacement, though I'm not sure how long they will do that for. It turned out that the fan noise was most likely caused by wires pushing on the fan, not the bearings failing, so now I have a spare.
Also note that this fan doesn't pull air into the inside, it just mixes air so there shouldn't be a concern about dust buildup due to the fan.
I replaced a single speed pump with a VSP when I added my RJ60+. I moved the motor power to the "unswitched" side of my timer and put the RJ60+ on the switched side. I set my VSP for 12 hours/day and then the timer for 10 hours/day -- one hour buffer on each side. Yes, the clocks will drift (and I will check them if I have a power outage), but I don't expect them to drift a whole hour in a single season. At the start of the next season I will have to set the mechanical timer again anyway since I de-energize most of that panel in the winter and I bring the pump inside so I will also have to set its timer. Just makes me feel more comfortable about explosions.