Idle temps don't really tell you much, as the temperature probes are horribly inaccurate at low temperatures. Run something like Prime95 or another benchmarking type program, and check the temperatures when at full load.
Yeah 40degrees idle is fairly normal, definitely within a normal kind of range. Without more info it's hard to know what (if anything) is amiss, but it could be something like a poorly seated cooler if you are getting dangerously high peaks.
Your case isn't an issue, though the two fans that come with it don't move a huge amount of air. This can be improved by adding a larger front fan (230/200mm is ideal, but a solid 140mm is still a good upgrade) and/or adding a higher quality 120/140mm rear exhaust fan.
As for compatible coolers, there is very little that isn't Prodigy compatible, nearly every cooler on the market will fit, one way or another. The qualifying factor is likely to be your motherboard, not the case itself, as each motherboard has it's own set of quirks which (potentially) limit cooler compatibility.