Cannot retrieve inport signal information

I have a huge simulator built with Simulink in a single template with some reference models. I need to generate code with Simulink Coder for just one subsystem. Thus, to save some compilation time, I have extracted the subsystem I want to generate code for, and placed it in a separate template. Previously, I have generated the necessary Bus Objects for the inports and outports of the extracted subsystem. So I can assign proper types to the inports and outports in the new template. I understand that this is the proper manner to separate subsystems.

At this point, I can generate code just fine with Simulink Coder. However, as expected, the generated input and output structures contain nested structures according to the composition of the Bus Objects.

I do not want that structure for inputs and outputs, I want plain structures. Thus, I place a pair of Bus Selector and Bus Creator after each top-level inport. Thus, the buses coming into my subsystem are now virtual. If I try to generate code, I receive the following error:

Cannot retrieve inport signal information for the selected subsystem.
Caused by:
Cannot retrieve inport signal information for the selected subsystem.
Dimensions of matrices being concatenated are not consistent.

If I try to generate code at lower levels, there are some subsystems for which I do not see the error. In particular, I get the same error when I try to generate code for a masked reference subsystem; but I do not see any error if I generate code for the subsystems at the immediate next level, i.e., under the mask.

I'm a bit lost because the error message is not very verbose, so I do not have any clue on what to try.