Cooler is always better.
Runing in the 40's at idle or light load is very good,
90+ is getting on the hot side but as long as you stay below critical it should be OK.
Do you have heatsink fans and chassis cooling configured for your chassis and elevation?
In the code update package the FRUSDR flash sets the fans speeds and therimal reagon information for the system.
Another tip is to make sure all the covers are on.
Some chassis do not cool well if the top is removed.
Bottom line, if it is getting hot, the CPU will throttle to prevent damage to itself.
You just lose on performance if the cooling is not good enough.