Technically anyone who spends more than 90 days in ANY EU country SHOULD apply for residency, and once you have spent 183 days you SHOULD be tax resident.
Thems is the rules. However unless you are a BRIT with residency in another EU country, you are only allowed to move around as a tourist for 90 days.

Most of the Germans, Dutch and Scandinavians I know aren't resident, but as you say, no border no check. (but there will be between Malta and Spain, Im assuming as it will be a flight) Ive had to show my passport before when flying between Germany and Spain (was in 2019)

Im assuming you have a UK passport? If so it should be stamped in any country other than the one you are resident in. (again what will happen is open to interpretation, mainly based on what day of the week, the colour of the border guards cat or what he has in his sandwiches today)

As far as I have been able to work out, if you are a resident in the Schengen area it should not be stamped anywhere in the Schengen area.

Border Control

Border Control

You don't have to show your passport for EU flights, you can choose to just show your ID card asuming it doesn't have any restrictions on it. Either that or your border guard forgot his sandwiches that day. I mention restrictions because British ex-pats in Italy are issued with ID cards that are not valid for international travel. I haven't seen anyone else's Spanish ID card so I don't know if it's the same.

Method of travel should be immaterial when it comes to checks on crossing internal Schengen borders. The general rule with Schengen state to Schengen state travel is there is no immigration control, so no passport / id card check except for when passing through airport security on departure, and nothing on arrival at destination.

There are exceptions under certain circumstances when borders are closed for one reason or another.

Whenever I've flown from Spain to another Schengen state (most recently to Amsterdam Schiphol in August 2020) the only place I have had to show my passport (for photo ID, it would not be a function of the airline staff to stamp it) is at the boarding gate (having checked in online, and there is no passport control at either the departure or arrival airport). Going through security involves showing a boarding pass, not a passport.

A lot of confusion is caused because airlines often ask to see a passport when there is no actual border security. I gave often been asked to show a passport at Gatwick and then walked freely from the airport as the flight was late night and there was no security at all. I suspect this won’t change.

Since both countries are in the Schengen area there should be no passport control in the sense of immigration control checks, as you are not leaving/entering Schengen.

I believe what you are referring to is a regular ID check that might happen during check-in, proceeding to the air-side of the terminal only for passengers, boarding, etc. But this isn't immigration control in that sense so not a border entry/exit check.

Or am I missing something here?

Airlines insist on photo ID to fly the most common form of photo ID used by UK citizens is passport as we don't have any form of national photographic identity card. I believe if one has one you can use a driving licence or other acceptable photo ID.? That isn't immigration but conditions of flying .