Honestly, if Rhaenyra married the Prince of Dorne, estabilishing the succession would be an headache.
Like, who inherits the Iron Throne and who inherits Sunspear? What last name do the children have?
Lots of messy stuff we would have to sort out in the long term.
Its only a headache in GRRMs bizarre fantasy world where each castle has been ruled by one house for millennia.
In reality, there's lots of different outcomes from the total merger of the houses (House Nymeros Martell already being a merger of two houses after all) and the firstborn child inheriting both titles, to Dorne agreeing to swear fealty to the Iron Throne but keeping their succession laws (so the firstborn inherits Dorne regardless of gender, but only the firstborn son inheriting the Iron Throne) to the above but without swearing fealty (so if the firstborn child is a son they stay unified a generation longer).
Which in fact is exactly what GRRM has written in case of the canon Targaryen-Martell marriage alliance
Daeron II was in a similar situation as we are now, and married the nominal
heir to Dorne, i.e. the eldest child of the reigning Prince. Instead, she was pushed from the succession spot in favour of her younger brother, who married Daerion's younger sister Daenarys.
Of course, this is probably not 100% applicable here as Qoren is
already Prince, but even then we could have a clause that he abdicates in favour of a younger sibling once we ascend to the throne (and we would be Princess Consort of Dorne in the meantime...)
Though not all options are practical:
to Dorne agreeing to swear fealty to the Iron Throne but keeping their succession laws (so the firstborn inherits Dorne regardless of gender, but only the firstborn son inheriting the Iron Throne)
If we win, the Iron Throne will have the same succession laws as Dorne. Viserys didn't intend this as a one time thing, apparently, but as a succession rule for the future: The firstborn inherits, son or daughter. So, the same as in Dorne. And even if it were otherwise, the eldest child being a son would still have the same effect anyway.
And yes, joining succession lines is undesirable. Local nobility is typically loyal to the local lord paramount house. That wasn't just a weird northern thing after Robb's death. You have the same in the Vale, where Harold Hardying will stop being a Hardying and take on the Arryn name once he ascends to the throne. In the background history, Houses Stark and Lannister have irregularily been continued through the female line at times as well, just to ensure a Stark/Lannister would rule the Westerlands/North. In fact, this has probably happened to every House in Westeros, as the result of having non-Salic male preference primogeniture (a daughter comes before a brother) but normally strict patrilinearity.
Like, speaking about "in reality", in reality only the English/British throne had those succession rules. Even for the English/British nobility, a brother came before a daughter, nevermind the mainland.
Exactly so as to keep possessions in the family line.
Anyway, point is - people are loyal to their established regional houses. Not to newcomers or imposed from above houses. House Targaryen ruling Dorne directly, Dorne becoming part of the Crownlands, would not go over well. Neither would be the kingly house being called Nymerios Martell. Plus, of course, there is a reason why Westeros has feudalism: We probably wouldn't even have the social infrastructure to run kingdoms directly. We
need vassals to run things; that's the whole point of feudalism.
