Can a model with Marksmanship Lvl2 elect to benefit from level 2 of the skill but not level 1 of the skill in the same order? E.g. a Spetznaz shooting a Bolt wants to ignore the cover penalty to hit but not have shock ammunition against the Bioimmune trooper.
Yes, both skills are optional and there's no obligation to use level 1 of a skill if you're using level 2, in fact with a lot of skills it's not possible (AD, C&H, CC Skills, etc)