I have three "coops" available from the run but none are left available all of the time. One is my main coop 8 ft x 12 ft. One is just a 4 ft x 8 ft shelter used in an emergency if I need to isolate one or more chickens. It is seldom used. Another is a 4x8 grow-out coop, used to integrate brooder raised chicks, isolate problem chickens, or as a broody buster as it has a wire floor. It has a run with it that can be shut off from the main run. Having this flexibility makes managing them so much easier.
The only downside I can see to having two coops open all of the time is that you will need to clean and manage two coops instead of one. If you feed and/or water in your coops you have more feeding and watering to manage. If they lay in two coops you may need to collect eggs in two coops instead of one. If you lock the pop door at night you have two pop doors to manage, morning and evening.
That extra work would bother some people but others not at all.