The 41 degree 960 EVO 500GB is a little hotter than normal idle for it but likely you were doing something. Have low thirties in two different boxes(one with it under motherboard).
But before all of that, file a bug report, i did one for ASRock Deskmini. Similar issue, reporting 116C, though on TMPIN6 only. Missing sensor. Dev responded pretty quickly.
Looking at your Zotac magnus link, it looks like the PCH is in middle edge of front of board. Between front HDMI and USB to right of it. Do you feel a ton of heat there? Like, 116C/240F, above boiling point of water amount of heat...
The Intel temp sensor is saying 40C, you can trust that. I would just ignore the other values as bugs unless you can feel/smell it.
As for noise, well its their custom box, if you don't like sound characteristics, nothing you can do. I sold off my Intel NUC5i7(highest model, 45W CPU) because it clearly was not designed with that much heat in mind. Fine for noisy office, not for home. Same with your Magnus 1080, it may be just fine during noisy game sessions and that's all it was designed for...
Bug Report and Program Improvement
If you notice a bug in a sensor report, or an undefined value, please select the "File" menu and choose "Save" to generate a complete report as a text file. Then, please email the file to cpuz[at]cpuid.com. Thanks !