Plus every now and then there are mods that come with different options, such as Vurts Flora Mod ex different styles of trees. So these shouldnt be DLed with NMM either
You picked the exact wrong example.

That mod actually has a version with scripts that let NMM users pick their options using a menu system during installation.
Otherwise you'd be right. Mods that have various installation options, unless specified in the description should probably be downloaded manually.