The HRE system is a really well done way of reducing autonomy; a slider and some unrest is the simple way. This is similar to how an event like the war of the roses is a well fleshed out revolt and the normal pretender rebel spawning is the simple way.
Going from a bunch of independent states to locked-in setup to all vassals to one nation is done through reforms, which are visible to outsiders, and a formal process - the result is a single nation with a firm central government... eventually, maybe. The problem here is not that the empire results in a 0% autonomy mammoth state with all the political leanings of the one who formed it. The problem is that the normal/generic integration process of vassals does not have all the pretty details of the HRE events, and is merely represented by high local autonomy eventually going away. OR the problem is that you didn't notice this happening the way you might notice someone integrate a vassal and only caught on when it was finished, similar to only realizing someone annexed a vassal after they'd had a chance to lower the autonomy.