I haven’t got any pop/click issues with Embedded at least within a past year or so. Update you are referring to is probably more to do with integration of HQPlayer in OS of SGC sonicTransporter rather than to do with code in HQPlayer.
But for pop/click, check first if you are getting overs - check the “Limited” counter in HQPlayer main window that it stays at 0 at all times (and that volume knob doesn’t turn red). If you are getting overs, disable Direct SDM in HQPlayer DSDIFF/DSF Settings if you have it enabled and turn down the volume enough that you don’t get overs anymore. But if you get those pop/click in quiet passages, then it is certainly not overs and you can proceed to next thing below…
If you get pop/click despite Limited counter staying at 0, problem is likely somewhere in the output side, for example something causing excessive latencies in the OS (typical sources of such being Bluetooth and WiFi adapter drivers). Also check that you don’t have any other endpoints enabled in Roon than the HQPlayer one.