@Scot ******
You might find some of the answers to your questions at this new website "Entry Thailand"
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I have not left or tried to re-enter Thailand during the Covid-19 era so the information I might have comes not from personal experience but from reading information online.
Does it take up to 30 days for Thai Embassy Malaysia to process an application for a TR?
Seems unlikely to me it should take that long, but I don't have any personal experience. I would guess it should take something like 3 business days, but again, just a guess. Maybe they're talking about the whole process up to and including the COE? Still seems like a long time.
Re Covid-19 extensions of stay. Earlier on in the pandemic immigration was very strict about granting this extension. You had to have a letter from your embassy requesting they give you one. That requirement dropped some time ago. It now appears that they give one to anyone as long as they request one and pay the 1,900 baht. You do have to fill out a form that indicates why you don't want to travel but as long as you check one of the options you seem to get the extension. A friend of mine got the covid extension very easily in Phuket, but she was already on a covid extension. I guess there are no guarantees, except it seems easier to get now. The last date they will be sold is 30 May, unless that date gets extended again...