Yes, AC11 will help you with inserting multiple stories in one go, but even AC11 will not have a solution for story height differences.
The guiding rule here is to have all files that have any hotlinked module relationship with one another have the exact same story height structure. This applies to the case where you need 3D that shows all buildings.
If you need all buildings shown in 2D, you might want to consider arranging e.g. the ground story plans of all buildings properly on a Layout. So, while they are still coming from different files, drawings generated from them are placed at the correct postions on the Layout so you get the output you need.
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