Kota Bharu is great travel down on a Saturday apply on Sunday and back to Thailand on Monday afternoon. Check they work Sunday to Thursday closed Friday and Saturday Muslim work week
As you have a multi entry you need to leave Thailand. Look at a cheap air ticket to Malaysia.( Air Asia or Lion Air) down and back in 1 day unless you want to spend a couple of days down there.
I recently did my 90 day report online and it was back the same day. It all depends on how many requests they get for the time it takes. First time online it maybe a little slower
From. Nakhon we have been several times to Kota Bharu consulate. Drop the application in on a Sunday and its back Monday afternoon. Penang is nice for a visit however visa applications can take 3 days. Kota Bharu you can get the early Train from Nakhon to Sungi Kolok and go across the border to Malaysia and get a taxi to Kota Bharu. If you arrive early enough lodge the form then hotel overnight collect your passport the next day at 2 pm