The differences between the two are more than cosmetic -- but the guns are both based on the original CZ-75 design, developed by the Czechs during the Cold War. It was that same "Cold War" that kept the Czech guns from being freely imported to the West.
Tanfoglio, an Italian firm, just started copying the design and selling them -- making changes as they went to simplify production. Because of the "Cold War" there were no legal ramifications to the Tanfoglio actions.
Tanfoglio makes almost all of the "CZ Clones,' including the Magnum Research Baby Eagles, the Jerichos, and others, including the EAA "clone" Witness line. The parts are just assembled in different countries. (EAA, for example, is an importer. not a maker.) The clones -- which aren't really clones (in the conventional sense of the term) -- are somewhat simplified versions of the CZ design. Some of the changes may actually be improvements.
There are lot of differences between the two designs, and only a few parts interchange between CZs and EAA guns (or the other "clones," like the Baby Eagle.)
Some mags interchange, but mags made for the Tan. clones often have to have the mag release notch enlarged a bit on the top side. (Some mags made for the clones simply won't work in the CZ -- they're too wide at the top, where the CZ mags tend to taper more.)
Grips don't interchange; barrels don't interchange. Most internal parts don't interchange, although some EAA parts (like slide stops and safeties levers) can be used in the CZ with modifications to the part or to the gun. Recoil springs interchange, but that's about it for springs -- as the other parts requiring springs are made differnetly (hammer, safety, trigger return, etc.) Pins are different, and the firing pin safety designs are different, as are the ways the firing pins are stopped.
Both guns fit one's hand better than most other guns, and are far more "pointable" -- just coming on target more easily than other guns.
Both allow either hammer down or cocked and locked first shots (unless you've picked up a "decocker" model -- in which case SA starts aren't possible. (The EAAs and some clones allow "safety on" while the hammer is down; but you can't do that with the CZ.)
Hi-caps are still available for both at reasonable prices.
EAA has had a poor reputation for customer service and warranty work, but they seem to be cleaning up their act. CZ's warranty and customer is right up there with Kel-Tec and Ruger, in terms of quick turnaround and friendliness.
If I were buying new and it was to be a primary gun, I think I'd get a CZ; but if I had other guns, and could be more forgiving about quick repairs (not that they would be needed), I'd let other factors enter into the decision.
CZs seem to be a bit more nicely finished and fitted. The EAA guns and the clones have many more suppliers of after-market parts and equipment. CZs are generally a bit pricier -- but good deals can be had with either if you buy used.