I don't know much about this, but the checks for valid PS1 CD, PS2 CD, PS2 DVD are done internally by the MechaCon when it detects a CD that is not Audio CD or VCD or a DVD that is not a DVD-Video. So I haven't heard of anybody managing to actually make the CDVD DSP read from a burned (backup) CD / DVD without it being of the above types considered valid by the MechaCon.
The only way that has been done has been through using a modchip to modify the MechaCon <->CDVD DSP bus signals.
The PS2 TOOL and TEST can read master discs, but they have a different MechaCon firmware AFAIK. Although nobody has actually been able to actually see the MechaCon firmware either, as it the most heavily protected part of the whole PS2 perhaps. Unlike on the PS1 MechaCon -
http://www.psxdev.net/forum/viewtopic.php?f=70&t=557&sid=65e6348a955a6a9de8504893b16afdac but this one is much simpler one and less protected than the PS2's in many regards (and also includes emulation for it).
And if you are thinking you could use the same method used on the PS1 - that won't work, as the MCU is totally different and a custom modification AFAIK. And even some software commands in PS1 mode that work on a PS1 don't work on it (the unlock command).
The PS1 has two serial interfaces - SIO0 - Controllers and MemoryCards (SIO2 on PS2 can be switched to SIO0 mode) and SIO1 - the serial port on the back of old PS1 models, which only has dummy hardware in a PS2 IOP AFAIK (and nothing uses it).
BTW, you can't access the SSBUS from the Dev9 bus, unless the transfer is targeted to/from the Dev9.
I am not sure, but doesn't POPStarter have other improvements over the bare PS1 mode, like more configuration, per-game patches/fixes, peripherals emulation, etc.? If so, then such an emulator is the way to go (given the bare PS1 mode limitations), though I would like it better if a homebrew one got better than it, like PS2PSXe, but that has not been developed for a long time sadly
http://psx-scene.com/forums/f292/ps2psxe-downloads-updates-105355/