The Super Varmint and CTR are basically the same other than the obvious cosmetic differences.
The real changes are the CTR using CTR/TRG magazines, the CTR having a lighter profile barrel and the Roughtech Super Varmint appears to come with a 2 stage trigger.
If you need 10 shot mags then the CTR is the way to go, unless you plan to change the stock in which case you'll probably be using AICS magazines.
The CTR barrel profile is more than heavy enough and less weight will be better for hunting purposes.
2 stage trigger comes down to personal preference.
As far as Mils vs MOA, definitely Mils.
They both do the same job in theory, but Mils end up dealing with lower numbers that are easier to interpret (seems stupid but it's true) and the reticles seem to be simpler in a Mil scope.
There are also more options for Mil scopes, so if you aren't used to either system may as well start with Mil.
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