Ok…say your at range 3 to your target, you roll two focuses, with Markmanship----first one goes to a Crit, second goes to a hit----the question is…does merc-co-pilot change the second to a crit also? My feeling is yes, although, I never did this in a game, I only modified natural hits.

what is the community's take on this effect?

If you have multiple effects with the same timing, you can choose the order to apply them in. So yes, this works just as you expect.