I believe you are talking about the Convert.Printer.SetPrinterName method?
PDFNet does not require the virtual printer to be the default.
What happens with the Virtual Printer, is PDFNet asks the OS to print "file.ext" to temp location "temp" using printer "X". Where "X" is what you pass into Convert.Printer.SetPrinterName.
By default the virtual printer is called "PDFTron PDFNet", but if you wanted to use a different name, then you would do the following.
1. Installation
Install the printer using your custom name. Convert.Printer.Install("My Virtual Printer")
This only needs to be done once, ever, but requires elevated permission to install the printer on the OS.
2. Tell PDFNet what printer to use
Now every time your process runs, you would statically call Convert.Printer.SetPrinterName("My Virtual Printer");
PDFNet does not change the users default printer, so perhaps something else is happening.