The engines were mounted well inboard to reduce the hazard of asymmetric thrust.
Four turbines are placed so close to centerline of plane that even if two on one side cut out, pilot has little trouble maintaining straight, level flight. [photo caption, p. 101]
The Comet's engines are snugged in so closely to the fuselage that there's no need for the customary trim tab on the rudder. [p. 102]
-- Francis, Decon. "I Saw This Jet Liner Fly 500 m.p.h." Popular Science, 156(5), May 1950, pp. 98–104.
Protecting against that hazard also explains the deflection of the engines' exhausts, which places them closer to a line intersecting the airplane's center of mass.
Another reason for the deflection could be to prevent jet blast from overheating or otherwise damaging the fuselage's skin just aft of the exhaust. The dH Ghost turbojets were built a decade before the first high-bypass engines, so their hot exhaust had no surrounding cooler air.
A third, faint, reason might be to facilitate egress from the over-wing emergency exit windows, sliding aft and down instead of climbing forwards. But avoiding asymmetric thrust is the reason that is documented in the literature of the time. (By the way, that entire Pop Sci article is a hoot.)