@ bager
I won’t go into a discussion about the engines diameters, but just one point: the afterburning part of the engine is always inside the fuselage, as its about as long as the engine itself. Only the nozzle is… well, at the rear end. Then, the M88, for example, uses a bypas system to reduce its IR signature, meaning, actively cools the AB canal by fresh airflow around it: the Ab canal is, nbasically, like “a tube inside a tube” so the external envelope of the rear part of the M88 is probably even cooler than the today’s A4 exhaust canal.
Of course, as you said, it wouldn’t be very interesting to have Ab canal “too short” (ending inside the fuselage), but, as you modernize the aircraft, you’d probably like to put inside something like a good radar, which would modify the nose (make it heavier), which you could, possibly make also a bit wider (to accomodate the radar) and slightly longer to put all the necessary electronic of the radars read end there. As a result you could shift the engine somewhat behind and, if necessary, even modify the rear part of the aircraft so that the nozzle is “outside”, even if somewhat under the tail (you could “cut” slightly the rear part of fuselage around it), so that it would look more or less like the F-104 on this pic:
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