That is correct, BUT as soon as your wife applied for and been issued the 1 YEAR Extension of Stay based on being over 50 years of age, which means she has long stay in Thailand you are able to apply.
NOT as you asked during the 90 days visits with a Non Immigrant O visa.
Buy an airline ticket out of Thailand, make your way into the airport, check in and pay 500 Thb a day with a maximum of 20.000 Thb overstay fines at passport control.
There is NO excuse to find which allows a person to go into overstay, there are over 80 Immigration Offices where a foreigner can report himself fo avoid the overstay. Hospitals do support with documentation and even staff to visit or contact Immigration in your name BEFORE a person get into overstay.
BE aware that getting caught will open another can of worms and that after 90 days of overstay, a blacklist period will be added to the fines
It is an Extension of Stay as mentioned in the stamp in your passport, not a visa.
It is not a visa problem that you planned to travel, you might go before you depart to the Immigration Offfice with support of your employer to apply for a NEW 1 year Extension of Stay and a NEW re-entry permit.
Tm47 is to confirm that you are on an address residing in Thailand, so it should be no problem to register that you are actually residing in Thailand on an address. Not sure what Covid has to do with staying at an address.