inner atu is much easier to use but will cause severe loss in coaxial cable is not well matched. using some unmatched antenna sytem with high swr betwen antenna and cable, cable loss may up to 10db or 20db....your machine is pratected but your signal is eat by the coaxial cable.
ts440, prc174, ft-1000 and others using these types of inner atu.
a seperated atu can simplify your antenna design.