Radial brake caliper compatibility?

Does anybody know anything about radial brake caliper compatibility? I understand that the bolt hole spacing has to be correct, but is there more to it than that? Brake rotor diameter matters I’m sure, but is that determined by the calipers in any way, or is that a specification of the forks? 

The reason I ask is because I need to buy some brake calipers for my ‘03 ZX6R forks that I’m swapping on to my Zephyr 550, and I’m trying to explore all my options. I chose the ‘03 forks specifically because the rotors on that model year ZX6R are 300mm, just like my Zephyr has. So I know the stock calipers would work, and I have heard that the ‘09-‘12 calipers are a direct swap and a better caliper. But I want to see if there are other options, mostly because I’m going for a certain look, and hoping to stick with Nissin calipers. Also because it seems like if I expand my search I can find better deals, since the ‘09-‘12 calipers are kinda pricey. 

The function of the brake is to reduce and convert velocity energy into heat energy that must be dissipated quickly.  Generally a larger rotor will allow more torque to be applied, which means quicker stopping by the same amount of force applied by the calipers.  But the best way to increase stopping torque is to go to a double rotor brake setup.  It will also increase the stopping stability because equal force will be applied to both sides of the wheel.  You can also increase the rotor diameter by using different forks, with a higher mount position for the calipers if you can find forks that will accommodate larger rotors.  Remember that rotor thickness is also necessary to ensure heat is dissipated quickly and evenly.  Usually, double rotor setups are thinner than single rotor brakes, so it's important to remain within the thickness specification if you want to switch rotors.

If you want to use calipers not specific to that particular model, you must consider not only the mounting bolt spacing, but also pad alignment with the rotors, both in terms of the radial distance from the axle centerline, and the lateral distance from the center point of the axle. You will also want the radial master cylinder to get best advantage of the calipers. 
If you have above average fabrication skills, you may be able to design and build some custom mounting brackets to use most any calipers. However, it is quite likely that any such adapter will introduce a little flex, thus negating much of the advantage of the radial setup.
I bet Brembo and HEL make a complete package for the ZX6R.  You may be able to find some lightly used ones if you shop hard enough.

I guess maybe I wasn’t clear or thorough enough in posing my question. I understand what the brake calipers do, and that the pads need to meet the rotors a particular way. The bolt hole spacing needs to match, but what I’m wondering about is if there are many variations in terms of the offset of the bolts to the rotor, and also the caliper base (where it meets the fork) in relation to the rotor. 

Look for example, at these calipers on Webike:  japan.webike.net/products/21203086.html#specification
They are listed as “universal” with of course the 108mm spacing that seems to be fairly common on radial mount brakes. But does that mean they will fit any bike with that spacing, regardless of rotor diameter? Webike doesn’t always give enough info. 

These are the brakes I would love to have, but new ones are expensive so I’m trying to find them used and figure out for sure if they would work. Or something similar anyway. I just don’t know if there are a bunch of variations in offsets between different 108mm bolt spaced calipers, or if they’re more or less “universal” and the differences are compensated at the forks. 

Looking at the link you have posted the "red text" makes ref to needing to "adjust" the mounting collars. My understanding is that you would need to get the collars milled down to suit the diameter of disc being used "not exactly a bolt on" solution. I think the critical part here is the spacing between the rotor and the fork leg as it would be tricky and probably ugly to off set the calliper on it's mounting point. You may need to space the rotors off the wheel to align with the callipers. If you go this route you will need to ensure the rotor is still cantered and supported by the raised hub on the wheel (if you extend past this all the load will be on the bolts and the rotors will run "out of true" both of which are BAD!!)

I am pretty sure we are talking about the same things. If there are other bolt on options, the ZX6R community does not appear to have discovered them.

If you want to blaze this trail, you will also want to consider the total surface area of the pistons and the surface area of the pads, clearance between the calipers and the wheel, and the location and orientation of the hose connection.