Code has been added (as of release 3.011) to bump up the output PDF version if a feature is marked as requiring a later PDF version (verCheckOutput call). The "bump up" of the output PDF version when a PDF of higher level is imported in some manner, is now handled more formally (verCheckInput call).
Regarding the issue raised above concerning cross reference streams, yes they are PDF 1.5. Since these should only appear in imported PDF files of version 1.5 or higher, verCheckInput() should handle it properly (i.e., the output will be PDF-1.5 or higher).
Note that verCheckOutput() is not automatic — it requires the programmer (of PDF::Builder) to be aware of the minimum PDF version required by a newly-added feature, and to add in the verCheckOutput() call. If any more PDF import calls are added, the programmer will need to call verCheckInput() for them.