A short update.
Altera support is now asking the software team, "whether this is a bug or a dedicated restriction in QII programmer".
Meanwhile, I did some additional tests and could see, why SFL fails. Briefly, it's because the Quartus programmer doesnt't operate the SFL Virtual JTAG function correctly. It's using wrong address bits and/or wrong VIR length (behaviour is different depending on the order of VJTAG instances in the design, but never correct, unfortunately).
The SFL function itself can apparently coexist with other Virtual JTAG functions, I was able to read the AS Silicon ID through SFL, using correct virtual JTAG instructions generated by quartus_stp tcl commands.
I expect, that the bug can be fixed almost easily by applying small corrections to Quartus Programmer.
Best regards,
Frank