ive seen this happen often. is it really that terrible?

I think its better. CO stilll boards by cabin and then rows, and somehow it works for them. US has tiny FC cabins, i cant imagine that 16 pax tops, delays boarding that much.

Also, ive seen this at other airlines, when flights are elite heavy (or zone heavy) agents alter the policy how they see fit, ie, US boarding FC seperate from zone 1 because 90% of the flight is in zone 1 or CO boarding by elite level, instead of all elites, because its IAH-AUS and the entire flight is elite.