@John *******
What is the part you do not understand?
The Work Permit has a valid until date and must be renewed before this date, one of the requirements is you must have a valid stay inside Thailand,
You did not have a valid stay inside Thailand, so you do not meet the requirements,
Then you try to convert your overstay into a valid stay, but applying for an Extension of Stay based on employment,
You did not meet the requirements, so application denied,
You waited to long to take action, it all should be done during your 90 day period of stay you got on your last entry, or you should have made a border run just before the end of March when all the information was that borders will close, to get a new 90 day period and more time to apply for the extensions of stay.