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I still think the paragraph at the bottom of page 7-9 on the link you sent me is a bit misleading, as it seems to indicate that .qsys files wouldn't be picked up. Maybe Altera could update this at some point.
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That paragraph is describing the ip-make-ipx convenience utility, and "the problem" is that although Qsys and the .ipx file syntax support it, ip-make-ipx ignores .qsys subsystem files as it searches. Perhaps the utility dates from SOPC Builder days, as subsystems are new for Qsys.
Working within the confines of what they have already given you, one workaround might be creating (.qsys, .ipx) file pairs where the .ipx file adds and describes only the .qsys "component", but I'm not really sure. I usually just use a version of the simplified file pasted earlier.
Good luck.