Anything that blocks or restricts flow to the engines will hamper performance.
At low altitude, the aircraft has sufficient performance margin that this is acceptable. However, engine performance drops as altitude increases.
They faced the decision:
Have no dust protection system -- the aircraft will have the best performance at all altitudes, but will not be able to operate in dusty environments without damaging the engines.
Always have the dust protection system -- operate in dusty environment, but suffer the performance penalty and limit the aircraft's ceiling and altitude performance.
Make the dust protection system removable and placard the aircraft that it shall not be operated at high altitude when the dust protection is installed.
To maximize operational flexibility, they went with 3).