No idea what they're waiting for. A visa extension though is fairly painless. Took me about 90 minutes and that was over lunchtime (which they don't seem to stop for)
This has nothing to do with the recent handful of stories about entry denials at Bangkok airports. Sounds more like badly trained staff at one consulate
I had a reservation for just before the 60 days was up. Technically, the extension is not guaranteed so it would make sense to have one on or before the 60 days is up.
Using a Green Bus rather than a minibus is not much cheaper - you may have to factor in a taxi trip to the bus station in CM and you'll need a songthaew in Mae Sai. If you get the cheap seats on the Green Bus, you'll save about 300 baht; in return you'll have a longer journey because the Green Bus stops at Chiang Rai en route and the police seem to stop them more than minibuses.