what valid reason does OP have? I don't want to be hard on him, but his situation does sound _exactly_ like what they brought this in for. Your son is a Thai citizen with a right to stay in Thailand just sorting out documentation so sure they will be more lenient there.
Anonymous participant 695 visas (with the sole exception of Elite/Privilege) are not generally intended to be revenue generating, that's just not the point of them. Point is to bring people into the country that will have some other benefit to the economy when here. A retirement visa is even cheaper than DTV, you think they are on thin ice?
you can get it either at the provincial immigration office, or the airport before you leave. Generally it makes sense to get it at the immigration office at same time as your annual extension but if you don't have one you can get it at the airport, just leave a little extra time.
you don't need to be a citizen. You need to be "resident". D7 Visa should qualify, from Google it suggests that once in Portugal you apply for a residence permit- this is likely what the consulate would want to see:
"This type of visa allows its bearer to enter and remain in Portugal for 120 days and request a residency permit with AIMA. This visa is valid for 120 days with 2 entries and, in most cases, comes with an automatically scheduled appointment with AIMA."
I don't think you will be able to do the 65,000 starting out, need to start with the bank deposit and then can move it later, after the first 12 month extension. Usually the money needs to be in an account in your name, not a company.
It may depend on whether you get the O or O-A. Advantage of the O is no health insurance required but it's only a 3 month visa. Then you need to extend in country and for that you need the 800k deposit.
O-A gets you one year and you can leave and come back at the end, for almost two years. Possibly if you start the 65k transfers immediately and keep them up for 12 months some immigration offices might let you have your first extension on that basis, if you were O-A. You need specific Thai health insurance in that case.
Residency is not the same as permanent residency, I don't think you necessarily need PR. Consulates will generally process anyone legally in the country who isn't a tourist. The thing they say about not accepting a specific temporary residency I think relates to the status Ukrainian refugees are on.
What visa are you on for Portugal? I'd at least ask the embassy, with what proof you have of your residency.
you can probably apply in Portugal, certainly you can if you are legally resident there, possibly can otherwise also. Some consulates will want proof of legal residence, some will deal with anyone physically in the country.