My understanding of the effects of the warm mod and presence mod are quite different.
I thought that for these, doug only modified the analog circuitry on the microphone inputs and did not modify the analog circuitry on the line inputs or the outputs. Thus, if the signal is fed via mic in (with or without phantom), the benefits of the warm or presence mod are realized. OTOH, if the signal is fed via the line inputs (RCAs on back), no warm or presence mod benefits will be realized.
Finally, to muddy the waters, it's my understanding that the mods performed by doug for the Transparent mod (tmod) DO enhance the line in (rcas on rear), unlike the pmod or wmod.