POD HD desktop converts the analog signal it receives at the guitar input into digital by utilizing the A/D converter onboard - I very much doubt the unit has 2 separate A/D converters for USB and SPDIF. For a DAW/computer to record the guitar signal (no matter dry or processed) the signal has to be digitized at some point, hence no way to avoid A/D conversion. Hence, it is not correct to call an A/D converted guitar signal "not truly dry". It is truly dry - the only difference is that one is "analog dry", the other is "digital dry", and both are "truly dry".
That's the A/D conversion referred to in the post with the "truly dry / not truly dry" discussions (the digital signal is converted back to analog to be routed to the L/R outs and headphones out only).
Both USB and SPDIF carry the digital signal so I guess the actual difference between the "dry over SPDIF" and "dry via L or R channel path over USB" is that the first is like as direct as possible in the POD HD and the second is passing through the amp sim / FX processing chain with all FX set to "no FX" or ie "bypassed", which may or may not affect the original quality of the already digitized dry guitar signal and also maybe affected by a potential crosstalk from the other channel path that has amp sim and FX turned ON. I don't know how significant or negligible this crosstalk is, or wether it is there or not but it may be there, potentially. Hope that helps clarify things, and definitely please feel free to correct me if I made a mistake anywhere in here