Unfortunately, at smaller stations often the same staff that mans the check-in desks will have to board the plane as well. So it's possible due to the s***show you described in the check-in lobby, it took longer than usual to finish check-in, at which point an agent was freed to run to the gate to do boarding.
Obviously what you described is not ideal, but it doesn't sound that different than some legacy airport operations at smaller airports where they've outsourced ground handling.
I've also seen situations where agents have limited hours in these smaller stations. Once had to wait on line to check my bag in Vegas which isn't what I'd call a smaller station but it seemed they had specific hours to keep the desk open.
I haven't seen the gate agent/ticket agent be the same person since 2010 in AUS. I've been to a number of smaller stations this year. The only thing I've seen outsourced on B6 are the rampers in HOU and MSY.