My printer was running with the top off for about a year, and with the filament sensor bypassed, and that was working fine. I did that to be able to print flexible filament at the time (ninjaflex and filaflex).Today, I installed the extruder upgrade (that should be able to drive flexible filament) and reinstalled the top.
And I had that knocking noise ! A lot of them. And inserting the filament was a pain. And one print had the filament completely blocked.
So I removed the top again, re-shunted the filament sensor, and I'm back printing.
My diagnostic is that the plastic part with the filament sensor has a wrong angle.
I might put the top back in place at some time in the future, but without the the filament sensor and support.