What are the reasons for an installed engine to produce less thrust than an uninstalled engine? Is this only due to the various flight conditions encoutered during operation, such as side winds and turbulence, or are there other reasons? Also, is interference between fuselage and power plant involved?
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.