I get that it was a complete non-title, considering the conquest of the Empire by the Turks, but that didn't stop them from taking 'King of Jerusalem' into their styles, and it seems to me like there would be a ton of prestige to be had in using a title they paid good money for.
I assume you're talking about Andreas Palaiologos and his practice of selling his questionable rights to other monarchs while in exile.
It's hard to say why something didn't happen, but here are some good reasons against it:
Andreas' "rights" to the title were tenuous at best. His father wasn't an emperor or even co-emperor and only maintained his claim while in exile from his legitimate position as Despot of Morea.
To the end, the position of emperor was not strictly hereditary. A claimant would be crowned by the patriarch and acclaimed by the Senate and army, both of which were unavailable and impossible to Thomas and Andreas. King of Jerusalem at least followed western succession laws.
For Catholic Christendom there was already an Emperor in Germany. It would be needlessly antagonistic to aggressively assert an imperial title.
After the deaths of Ferdinand and Isabella, Spain would be ruled by a Holy Roman Emperor in his own right, Charles V.
They did in a way. In all documents to the Council of the Indies, or at least directed to Charles I of Spain (Charles V of the Holy Roman Emperor) the heading was SCCM. While the Sacred Caesarian Catholic Majesty doesn't appear very often for Philip II, some used it out of habit. I work on pre-1556 documents so I cannot attest to the frequency of this, but I have seen a few that did.