I got visa exemption when arrived to Phu Quoc. Now I want to fly to Hanoi and they want mainland visa in Phu Quoc because it is domestic flight. I have visa invitation letter for Hanoi but it's not valid. It is possible to get mainland visa from travel agent in Phu Quoc airport in 30min but it costs a lot, procedure looks very strange (although it worked for me) and seems to be the only way. Is there any other way to get mainland visa when I already have Phu Quoc visa exemption?
There is only 1 option for you in this case: you need to contact with either the Immigration Officer or the travel agent (as mentioned) to get them process the mainland Vietnam visa in Phu Quoc for you.
You can save money by getting Visa on arrival for Vietnam (with cheaper price) before departure to Vietnam, but once you enter Vietnam, you cannot use that method (source.)