As I said, there's a difference between being a victim of rape and a hostage (unless you're both)
Even if stockholm syndrome can be extended to victims of abuse, it can only be extended as far as when the victim is a hostage (individual who cannot escape a relationship for the fear of their safety and so due to this and an innate survival instinct, they develop an attachment in order for their security to be guaranteed) and when the abuser is the captor (and individual who physically and/or psychologically abuses the hostage and threatens them to stay in the relationship).
But in this manga, the alpha isn't a hostage because he was never in a relationship with the enigma in the first place. The rape was a one off thing (hopefully) and even if he develops feelings, it isn't stockholm syndrome because he never to fell in love for the fear of his safety.
You could theoretically apply Stockholm because the alpha is raped again in a later chapter and is then blackmailed into “relationship” of sorts with the enigma. What the OP likely means in the case is “Conditioning” more so than Stockholm for the most part. The alpha is exposed to his rapist over numerous times and beings apply emotional responses to either violent act or the violator themselves thus creating a bond of “affection” turned love. Despite this none of this romance in the traditional sense and is still a form of emotional abuse.
Don’t put the romance tag if it’s a rape