Custom Refs are almost always used for non-configuration based files like word docs and pdf's. I suppose you can do it the other way though and attach a part to a pdf. I checked the API notes in 2017 and didn't see anything there so I doubt there's anything coming. If you really need this then you can look into the table XRefConfiguration where you can see what configuration is attached and modify it if you're bold enough. Make sure an enhancement gets created for this as well.
>>Custom Refs are almost always used for non-configuration based files like word docs and pdf's.
Do your PDFs reference your drawings or do your drawings reference PDFs?
I use to have the drawing reference the PDF, but felt that wasn't quite right. So now the PDF references the drawing, and the drawing references the model.
Within my World a configuration in a part/assembly can be another separate part. I then intercept drawing check-ins and initialize each configuration (i.e. sheet) with its corresponding part (title block) information. It would be nice if a PDF could reference the actual sheet it renders. Currently I just store the config name in the PDF as an EPDM variable.
Display --> Options --> uncheck "Set focus to active configuration"
A lot of bad things can happen.....not "only"
Make sure your data card doesn't have "update all configurations" on the variables you wish to control differently in different configurations.