Just starting to play with Shooter and have yet to use this function but have played with it in Loadbase but I don't shoot powder that varies that much in my LR rifles so don't use it much.
From the manual.
MV Variation - This is an optional input, but if you input this field, you also need to input the Powder Temp field for it to be of use. You can specify the amount of variation of Muzzle Velocity per degree of temperature change of your powder. This is something advanced shooters probably know after collecting this data shooting under several different temperatures. They may see that they chronographed avg 2850fps @ 55deg and 2855fps @ 57deg and 2860fps @ 59deg. So they could enter 2.5fps here. Temperature has varying effects on each kind of powder and it's not always perfectly linear so this option is just a "better than nothing" approach.
Powder Temp - This is an optional input and should only be entered if you also entered an MV Variation. This is the base powder temperature and should coincide with your Muzzle Velocity. So as in the example in the "MV Variation" field description above, you'd put 55deg here and 2850fps in your "Muzzle Velocity" field (or you could be 57deg here and 2855fps in Muzzle Velocity, doesn't matter). Now when you run a calculation using this ammo profile, there will be an option to enter current Powder Temp. If you were to specify say 65deg for powder temp, Shooter will automatially raise your MV to 2875fps.