In reality there are all kinds of various degrees of authority over a piece of land and its peoples. In the game you're either in or you're out of the Empire. Formally the kingdom of Italy was part of the Holy Roman Empire even after 1648 but apparently your video decides that's when they no longer can be shown as that
Already by game start the Empire had a questionable authority in northern Italy and this only got looser as things progressed (and remember this is for an organization that's not really the biggest on central power to start with in this era).
The Italian states are removed from the empire because they had by that point become members in name only. They did not participate in the imperial diets, they would not belong to any Imperial circle when those were conceived, they did not really obey the emperor on the whole and they had already decisively defeated the emperor in war when he tried to impose his authority on them again already before the game starts. During the Italian wars it also became pretty clear that the Empire didn't really bother to try to protect the Italians (we do have an Emperor that did end up subjugating northern Italy in the timeline, but even then he chose to have the lands ruled from Spain rather than under Imperial princes).
You could argue that they should in fact start outside the empire as most of the above is just as true in 1444 but the way we have it now allows you a certain time to re-assert your authority over Italy if you're playing the emperor but unless you're willing to spend resources and quickly you will lose your authority over the region and others will see that and start eyeing it greedily.
EDIT: So to sum up. History is the bigger reason behind it really.