Ok, so it seems you are reporting two issues. One about printer paper tray, and another about some virtual printers not outputing the expected page dimensions.
PDFNet does not support Tray selection, that would require you to configure the printer yourself. See this forum post (last paragraph) to learn more.
The same is happening when printing to a virtual printer like PDF24 PDF
PDFNet is generating PDF pages as exactly specified, and other printers, like Microsoft Print to PDF output a PDF with the your selected page size, so if PDF24 PDF is not that would be an issue with that virtual printer. Perhaps a similar solution to the tray issue would also resolve it.