I had a similar issue back when first adopting 2016... The behavior I observed was that even though I used DWG to PDF, I'd get a different resultant file size, and PDF settings (i.e., Layers, etc.) when printing the PDF in different ways (i.e., Autopublish, Plot, Publish, PdfExport, etc.).
What I found, was that in 2016 version Autodesk hard-coded some of the plotting mechanisms to use one of their new PDF driver, even when a named Page Setup specifies DWG to PDF driver.
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What I did to fix this -
Go through your local copies of their new "
AutoCAD PDF (<SomeDescription>).pc3" files, make a BAK copy of the originals, and then try setting all of those PC3 files to your desired DWG to PDF settings... Assuming the default Printer Configuration Search path in Options, that would be here:
Code:
(startapp "explorer" (strcat (getvar 'roamablerootprefix) "Plotters"))
HTH, Cheers