Is ~49 °C normal for motherboard idle temperature

Your mileage will vary. A cooler can only cool the CPU to whatever the ambient room temperature is, at best. My CPU at home is a Phenom II and it runs OC'd @4Ghz and typically is in the mid-high 50's. 32c is quite good i'd say. The thermal max (where it shuts down to avoid damage) Your cpu appears to be rated up to around 60c before issues happen. I'd say you have nothing to worry about.

Prime95 is intended to generate a TON of heat, so while it's a great test for load-testing, its not a representation of what you'd expect in "real life" use.

1: 51 degrees C is a bit warm but nothing to get too riled up about. This is frequently the Northbridge temperature and since your specific motherboard doesnt have a fan on the northbridge it makes sense the temps would be a little higher than normal. To put the temperature into perspective the i7-4770k processor that you have is stable well into the 80 degree Celsius range (but not recommended).

2: The sys Temp. as I mentioned is usually the northbridge.

3: The northbridge is always working, even when you think the computer is idle, all the disk IO, graphics, Wifi etc, run through there, so it's always doing something.

It would be fairly trivial to add a fan or reposition an existing fan to make sure the Northbridge is getting enough airflow.

I would recommend adding a small fan that blows over the northbridge, but it's probably okay without it also.