yes they refund the merchants fee. All the atms charge 220 baht per transaction, but some let you pull out only 20k and others upto 30k. If you use krungsri you can withdrawal 30k per transaction it's the yellow bank/atm.
Company account doesn't work for the 500k requirement. You have to have 500k thb or more in a personal account not company. You can then show the deposits to that personal account from the company account.
You'll need 800k thb for the first year regardless. If you make international transfers monthly above the minimum requirements you can switch on year 2, however make sure you transfer more then enough to account for currency conversion shifts.
Depends what province you're in. If it's chiang mai go to the immigration office next to the airport. They have a drive thru and walk up window left side of building just for 90 day reports.