Basically that, yeah. That's why, in 99% of (non-player) HRE cases, when you run the EU4 convertor, it transforms into a mess roughly approximate to EU4
anyway. Barring, of course, the potential of (I dunno) Bavaria being a bit stronger and larger than usual. Maybe a few less independent cities and such. It's still a mess, and in some ways, a bit more of a mess with the various royal marriage shenanigans the AI gets up to.
It's represented as a unified state on the map, and a
player can most certainly make it one in fact as well as in appearance. But most AIs, if it doesn't just collapse into infighting that makes the 30 Years War look tame, will have it a mess like the historical one in EU4. Just without the pretense of 'unity' on the map.
(the same also applies to
any big Empire in CK2-to-EU4 that hasn't centralized enough, from the Byzantines to the various Caliphs to Scandinavia)
EDIT: Relatedly, EU4 just models it differently, even if it is the same thing. The HRE system in EU4 can be looked at as a cludge towards mimicking the 'king ruling over a bunch of unruly vassals' of CK2 in a lot of ways.
If not for the fact the HRE system is a holdover from the even
older EU3, I suppose
