Thank you for your interest in Freestyle.
Yes, you are experiencing these limitations because you are operating on a dwg file that was not created in Freestyle.
Freestyle will not let you modify original drawings nor change the drawing size in dwg files created in other programs, as you mentioned Freestyle will show original drawings in a non-editable layers grouping and the Options dialog will have the original drawing properties grayed out.
You can add notes though; Freestyle will save your notes on a separate layer.
I’m bit intrigued by the problems your are having with saving your dwg file in pdf.
Would you be able to provide us your dwg file so that we can have a look at it?
Regards,
Avto Chachava, Autodesk Product Support
Avto Chachava
Autodesk Product Support
Autodesk, Inc.