Windows vs OS X temperature, Windows runs hotter I could see about 10 degrees celsius less when idle in OS X, compared to Windows 8.1, that's ~49 °C compared to ~38 °C.
I've seen that, according to Macs fan control, the fan is shut down in idle, but after googling, some people say macbook should always keep fan running at around 1200 rpm. 

Should I leave it as is or would it be safer to use a custom fan management to keep it running at 1200 rpm?

Specs: MacBook Pro Retina 13" 2015
I would not recommend changing you fan-speed management if you are not sure about it. 38°C - 49°C won't harm your macbook.