Currently if you are using the Sheet Layout workflows and using the Print Plan Set command to create the PDF file there is no Layer Control in that process as it stands today. I have an enhancement request in the system today for this so it is logged as a request at least.
If you use the Create 3D PDF from a View (Plan View or Sheet View for example) then it does pass Layers and Surfaces and Images out and when opened in PDF Reader it allows you to turn those on and off - after opening the PDF File, you have to click onthe Page of the 3D PDF and it takes a few seconds - then you can turn on Layer controls and then turn objects on and off etc. This may solve the issue that you are trying to solve.
Alan