Can you have non-altera devices in the Intel Quartus Prime Software JTAG Chain?

​You can add other devices (non-Intel/Altera) through the programmer. Open the programmer then select the "Add Device" button on the left side. A dialogue should appear that allows you to pick from existing devices. Use the "New" and/or "Import" buttons in that dialogue to add new devices. Essentially the programmer needs to know the device's JTAG ID, instruction register length, and the name you want to give it. Once you do that (assuming you get the JTAG ID right) the programmer will recognize the device and automatically issue a JTAG bypass instruction when it appears in a chain.