It would require Victor Emmanuel II to have a very different character than he did IOTL for him to really consider this possibility. The reason that Kings such as James V of Scotland and Ferdinand II of Aragon ruled Kingdoms that remained separate legal entities was due to the fact that the legitimacy of their rule was based upon inheritance. That was why even when they held the thrones of England and Castile, respectively, they wore two crowns and their kingdoms remained separate legal entities in law.
Victor Emmanuel II set out to unify Italy under his dynasty by right of conquest, and to a lesser extent as self proclaimed "Father" of the Italian people. Had Victor Emmanuel II had the same ambition, but had a more legitimatist mindset, he could have potentially undertaken the same actions that he did, but kept the old Italian kingdoms and duchies legally distinct. This would have involved himself declaring himself Emperor of all Italy, and receiving homage from the now reduced Italian rulers such as the Bourbons of Sicily.
Such a path would have made Italy more superficially similar to the Imperial Germany. However, there would be significant practical obstacles to this course of action, not the least of which was the Austrian Emperor, who would have been unwilling to sacrifice the crown by which he held northern Italy, and pledge his fealty to an "emperor" who he considered to be his inferior, and a usurper to boot. The Pope in Rome would also be a difficult ruler to co-opt, unless Victor Emmanuel could convince him to establish a second "Holy Roman Empire," in which Victor Emmanuel would be crowned by the Pope as a secular ruler, while the Pope would retain his spiritual office, as well as retaining temporal power in some kind of convoluted arrangement.
To return to the original premise, it would not be impossible for the Two Sicilies to remain a legally distinct kingdom under the authority of a a Sardinian "Emperor," but for that to happen would require a radically different character for Sardinia's monarch. My own opinion is that a decentralized empire would have been much more suited to governing Italy than the centralized monarchy that actually came about.
What are your thoughts?