As someone who have been around jets, F-111 and F-16, I can say that this story is of zero help. What is this 'rain cover'? Anything that is attached to a jet that can prevent flight is usually tagged with that famous 'Remove Before Flight' red streamer. So what is this 'rain cover' thingie the article was talking about?
Now here is my suspicion...
It has been reported that a British F-35 pilot realised the rain cover was still on and tried to abort take-off but was too late to stop the jet before the end of HMS Queen Elizabeth’s runway.
The pilot ejected, that mean the jet was moving and building up speed.
Modern avionics depends on air data via the pitot/static probes.
Elevate Unmanned Flight: Pitot-Static Probe for Airspeed and Altitude in Extreme Conditions. Ideal for Aviation and Wind Tunnel Applications.
www.aeroprobe.com
en.wikipedia.org
There is something call the 'Central Air Data System' computer or CADC.
Description An air data computer (ADC) is an essential avionics component found in aircraft. This computer, rather than individual instruments, can determine the calibrated airspeed, Mach number, altitude, and altitude trend data from an aircraft's Pitot Static System. In some very high speed...
skybrary.aero
The flight control computer (FLCC) can also have the CADS inside it as a subsystem, but usually, the FLCC and CADC are distinct units in the avionics compartment.
If the jet is static, pitot (ram air) would be zero and static would be something like 29.92 baro or whatever pressure above sea level. On the takeoff roll, static pressure would not change but pitot would change. Now the CADC and FLCC begins to work together to calculate various flight control responses, namely, we have a changing variable -- ram air. Then once the jet is airborne and gain altitude, static baro pressure would change and the FLCC and CADC would have a second changing variable. And so on and on...
Now, you can do keywords search for 'F-35 pitot tube' and see where the jet's pitot/static probes are located. Each probe would have a 'rain cover' with that red 'Remove Before Flight' streamer attached. It would be absolutely ridiculously bonkers to have the ground crew and the pilot to miss two red streamers. If this is true, the pilot should have his wings removed and probably cashiered out of the service, and the ground crew decerted. The pilot is one person, then we have the crew chief and the assistant crew chief, then we have someone on the fire watch, so we are looking at several people missing the two red streamers. I doubt this is the case. There has to be something that affects the critical air data component that can be seen only after the jet is moving. The F-35 flight data is projected onto the helmet's visor so that mean the pilot could have noticed airspeed zero as he is on that takeoff run. My opinion is that the words 'rain cover' are misleading given understanding of basic avionics air data system knowledge and how ground operations work. Am just speculating here but I think am on the correct investigating path.