Yes it will. The leveling system is made so that it doesn't have to be used to make the rest of it work in another setting. Hard to explain without crossing over my NDA agreement, but suffice to say, yeah, the CoH material will still be compatible with other Unisystem game lines.
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Jack: "Goddamn Brenda explodin' like a water ballon and worms drivin' my friends around like they're goddamn skin-cars! People are spittin' acid at me, turnin' you into cottage cheese, and now there's no f*ckin' goddamn Mr. Pibb!"

Bill Pardy: "Jesus Christ, Jack, let me get right on it!"