It depends totally on what kind of "100 chickens" you want. If you wanted a single flock, e.g. 100 layers to sell eggs from or a really large breeding flock (possibly subdivided) of a single breed, then my best suggestion is to look at OLD coop designs, like 1900-1930ish, when there were lots and lots of small commercial flocks of like 100 hens and the technology was pretty well worked out.
If you want to keep a bunch of breeds separate, though, you can subdivide a 100-hen coop up to a point, but if it's going to be a bunch of 3 or 10-chicken units (say), then you are probably going to have to look at other designs.
In general it is much more efficient to have a single building, save you time and money and labor and aggravation. I am not super convinced that the biosecurity thing is relevant to normal backyarders, unless you will routinely exercise excellent personal biosecurity when going from coop to coop (disinfect shoes and hands, change clothes, that sort of thing) -- but there *is* definitely advantage to having somewhere separate you can quarantine birds or isolate them if needed.
Really there are a lot of different 'best' designs, depending on what you want your flock(s) to be like and what you want to do with them.
Good luck, have fun,