Does my Thai spouse need to accompany me to apply for an annual extension of my Non-O marriage visa?

Yep, the reason for your extension <- in your case your thai wife HAS to be there with you when you apply for the extension,

she doesn't when you go back to get the extension inked in after the 21 day under consideration stamp runs down though, so just one visit there with you

I would say without her you're not gonna get the extension 😮