What are the reasons for an installed engine to produce less thrust than an uninstalled engine?
No, these losses are well known and are called installation losses.

Their reasons are:


Intake losses. In a ground test the engine will be fitted with a screen to avoid foreign object damage, but none of the long intake tubes which are common especially in supersonic aircraft.
Generator loads: The engine drives generators to supply the aircraft with electricity. This can be simulated in a ground run, but often the generator load is higher in flight.
Bleed air: Some of the compressed air inside the engine is piped to a heat exchanger and then into the cabin for pressurization and heating, or used for leading edge de-icing. Again, this can be simulated in the static test but sometimes bleed air losses are higher in flight.


Interference between fuselage and power plant is only to be expected with fuselage-mounted engines. This can be both beneficial (as in the precompression at high angle of attack and speed on the Rafale or the F-16), or it can distort the flow when side-mounted intakes are operated at a high sideslip angle.