An independent Transylvania would have made no sense. There is no such thing as a "Transylvanian" nationality. [1] You either give it back to Romania or let Hungary keep at least some of it (as in the Second Vienna Award). There are three reasons why Stalin would be likely as in OTL to favor Romania:
First, the Romanians had switched sides in World War II and declared war on the Axis. (Hungary tried to do so, but without success.)
Second, not to restore all of Transylvania to Romania would look like validating an award brokered by Nazi Germany and Fascist Italy.
Third, though the Romanian Communist Party was smaller than the Hungarian, Stalin considered it more dependable--the Hungarians were notoriously faction-ridden, had been heavily purged in the 1930's, were riddled with police spies, etc.
The closest thing that Stalin came to recognizing the Magyar/Szekely minority in Transylvania was pressuring Romania to create a Magyar Autonomous Region in 1952. As Doug Muir noted in an old soc.history.what-if post "This was sort of Stalin's version of the Vienna Award. It was a sop to the Hungarians, it preserved the image of Socialist Internationalism, but most of all it kept both satellites on their toes -- the Hungarians thinking they might get Transylvania back, the Romanians fearing they might lose it."
https://soc.history.what-if.narkive.com/afArlACL/stalin-lets-hungary-keep-some-of-transylvania
[1] You can of course argue that there is also no such thing as a "Moldavian" nationality, but pretending that there was at least served a purpose for Stalin--a justification for getting Bessarabia back.