The wing root mounting was first seen on German bomber projects in the early forties - with up to six engines. Those projects later progressed in Russia and became the Tu-16 Badger bomber and the Tu-104 and Tu-124 airliners. In America I think that the Northrop YB
-49 bomber was the only attempt (excluding early fighter planes).
With limited engine diametres this mounting method had obvious aerodynamic and structural advantages, but also a vast number of disadvantages as already mentioned.
One further disadvantage is that the engines take up much needed space for fuel tanks and landing gear.
Tupolev solved that problem by putting the landing gear into separate pods.
DeHavilland put separate fuel tank pods on the wings of later longer range Comets.
The Avro Vulcan bomber had a very thick and wide cord wing with room for everything (except passengers of course).
Another disadvantage is that as jet engines evolved into much more efficient turbofans, then they also became more sensitive to disturbed airflow into the intake, or you would risk a compressor stall. A side slip (e.g. caused by turbulence) at high altitude and high Mach number on a Comet or Tu-104 style plane would not be healthy if equipped with most modern and highly efficient engines.
You see a little of the same principle on trijets like B-727, HS
Trident and L-1011. They all had slight performance loss on their #2 engines and higher probability of compressor stalls. The DC-10 and MD
-11 went to quite some structural disadvantage to eliminate that slight problem.
It will be interesting to see how the BAe Nimrod Mk4 will perform with new BR715 engines, when they are ready for flight in a couple of years. But then, as the military planes they are, they won't scare the hell out of 200 pax if one day they should suffer a compressor stall.
Kinnd regards, Preben Norholm