I took these dimensions from the specs.  This means the coop section is about 45" x 68".  About 20 square feet.  I could not find a photo that gave a good shot of the inside layout but the roosts at least are higher than the nests.  There are three roosting bars, each probably 45" long.  The nests are internal to the coop area. open nests with a roost section running over the.  They can poop in the nests from the roost.
| Foraging or Run Area Length | 81.1 in. | 
| Foraging or Run Area Width | 68.7 in. | 
 
You are in the cold midwest.  That means you will have days this winter where they will not be able to go outside.  That's when the size of the coop becomes the big issue.  In the summer you can probably work around that.  It looks like that run section would be pretty predator proof if you stop digging predators, maybe by adding an apron. So you could leave the pop door open so they have all the room in the run available when weather allows.  I could not find the size of the wire openings, can baby chicks get through those?   
It looks like the coop section is raised off of the ground just enough for mice, rats, or even a snake to make a permanent home under there.
That height is probably to the peak.  I think it would be uncomfortable to stand or work in there.  
I do not think this coop/run would be suitable for a permanent home to adult chickens the way I think you want to use it.  It could work as a grow-out coop to help integrate the chicks.  If you can run electricity to it you could even use it as a brooder.  You might need to line the bottom of the fence with wire mesh or netting to keep the young chicks inside.
Can you train two different flocks to free range together and sleep in separate buildings at night?  Maybe.  Some people do that successfully.  It's also possible they will al want to move into the same coop to sleep.  When they free range they are free, they can do what they wish.
You said you wanted to put one specific rooster with certain hens.  And let them all free range together.  That may not work out quite as you plan.  What is happening now with the two boys?  Do they hang together during the day or have they split the current hens so each has their own harem and hang out in separate territories?  Most of the time they choose separate territories but with living animals about anything can happen.  I have seen two males hang together with one harem while a third had a separate harem and his own territory.  They were all able to sleep in the same coop.  
When you integrate the new girls and they reach a certain age I'd expect them to pick who they want to hang with during the day.  They could split up, some to each boy.  They may all stick together with one boy, or they may just form a separate flock and ignore the boys.  Or come up with some other combination.
So what would I do in your situation?  I'm not sure how those boys will be able to continue getting along so there is some indecision for me.  I'd build a coop big enough for the entire flock in your midwest winters.  You say you want to hatch chicks so include them in your entire flock numbers.  I'd build it at the other end of one of your current runs so you can tie into it.  Keep your current coop as a nursery to help with integration, maybe a place to isolate a chicken if you need to, maybe even try to train one of the roosters to sleep in it with his harem if the two boys can't share a coop at night.  A separate coop/run can come in handy in so many different ways.  It gives you a lot of flexibility when things happen.  
I personally would not buy that prefab coop, I think you will be better off spending your money on a more permanent solution, a coop big enough for your needs.
Good luck!