Can airlines prevent me from flying in this complex situation?

Question

My 2-entry D visa is valid for 4 months

I have a SEF (immigration and borders service) appointment for a residence permit, 2 months after the visa starts.
After the SEF appointment, I plan to leave the Schengen area and come back to Portugal on the week (preferably on the day) my D visa expires.

They usually take 3 months to issue residence cards at my SEF office.

Time spent in the Schengen area in the last 180 days as of last week of the visa : Less than 2 months.

I'll have an A4 PT document which is a proof of application for residence permit.

1) Would airline or border agents cause me trouble? My passport isn't liked by the EU and doesn't have visa free access to Schengen area. So, I'm a bit worried.

I think border agents of Schengen area can see that I applied for a residence permit using their system, but I'm not sure.

There are a lot of people who are stuck in Portugal. They can't leave because if they leave their residence permit becomes useless. This is the case because they couldn't renew their residence permit after their current one expired. As a "solution", Portugal gave extensions until end of 2023 for such people but that's only recognized domestically. I know of people who missed funerals because of this problem. As a positive thing I should mention that Portugal doesn't discriminate passports. The guy who missed the funeral was an American. Anyway, my point is I shouldn't trust Portugal to update their system in a timely fashion. This means border agents of Schengen area might not see my residence application on their system because the system relies on the data Portugal enters.

Direct flights to PT are quite rare.

2) Even if border agents are ok with this, can the airline create problems? Not sure what to do about this? Some airlines requested return tickets from me even though the country I was flying to wasn't requesting one from me, and it was visa-free.

Answer 1

Time spent in the Schengen area in the last 180 days as of last week of the visa : Less than 2 months.

Irrelevant in the case of a D visa/Residence Permit, as stays in the issuing country are not counted against the Schengen clock

This means border agents of Schengen area might not see my residence application on their system because the system relies on the data Portugal enters

Until the EES (Entry Exit System) is rolled out later this year or next year, there are no global systems for those purposes.

A non-Portuguese border guard will only rely on what you actually present physically, be it a residence permit, a visa, etc. A Portuguese one may check in some databases for the Residence Permit, but this is not widespread

Direct flights to PT are quite rare.

If this is a possibility, you can transit through Turkey, the UK or the middle-eastern states, they all have direct flights to Lisbon or Porto and have (all but the UK) very lax visa requirements for transit.

can the airline create problems

Of course, they can, but wrongful, denial of boarding, i.e. you did have the correct paperwork, but they still deny you boarding, is, if you are taking an EU airline (Turkish and Emirates for example are out of the question, even though the Turkish civil aviation authority has a similar policy), very expensive for the airline in compensation (EU261, up to €600), so they better not deny you for invalid reasons