if you're working in Thailand, even if it's strictly online for an overseas company you legally require an appropriate visa and work permit - full stop. That they turn a blind eye to those who don't is a different consideration. You don't have to believe me, here's the Chiang Mai Labor Office explaining it
Those from the Philippines quality for visa exempt with 30 days on entry (possibly 45 now with the recent proposed extension). Visa on arrival is a different form of entry - yes, VOA is not currently available but that doesn't apply here.
As others have noted, she'll then have to do 14-days "home quarantine" (the official term used in English) upon traveling to Chiang Mai.
even before I had two year visa extensions and a work permit I was always looking out, well before COVID as to the best way to stay here long term legally for longer periods and I've been through multiple visas since 2013 :)
I don't want to be unfair - there may be a few who are legitimately stuck here but many of these people are not even trying at this point. In Chiang Mai, it's not that expensive to enroll with a Thai language school or even a self-defense class with the equivalent of a year-long ED visa (90 days + 3 x 90 day extensions) if people really wanted to stay without drama. For those over 50 I believe Non-Imm O's are available within Thailand now as well.