Here's my experience with having two coops.
I initially built a second coop to house two roosters who wanted to kill each other, and also to keep them segregated from the flock for purposes of keeping the peace.
As time passed, one was killed and the other died of illness. When it came time to add chicks to the flock, I installed the five new Welsummer pullets in the vacant coop. Meanwhile, four Sussex hens became problem feather pickers, so I moved them into the second coop since it had already been partitioned off to keep the two roosters from mixing it up. The Sussex have their own run coming off an entrance to their section of this coop.
This past spring, I anticipated getting more chicks and I moved the five Welsummers, now hens, into the original coop with the majority of the flock. When the new chicks became old enough, I moved them into the half of the coop shared by the Sussex on the other side.
Now, two of the Welsummers decided, on their own, to move back into the coop they were moved out of to make room for the new chicks. Everyone is getting along just fine in spite of the age differences.
Over the years, I've had hens decide to sleep in one coop and then a few weeks later, they will move back into the other one. Usually they seek a change when they encounter too much conflict at roosting time.
So, having two coops is a real blessing, if you don't count having another coop to keep clean.
Yes, roosters will indiscriminately mate with all the hens in both flocks. That's a given. Other than that, having two coops shouldn't present any problems with the flocks.