Maybe I'm mis-understanding the whole "non-transparency" issue. I see non-transparency as saying that you must distinguish between the effec and the underlying source of the effect.
The way I see it, Detect Scrying would detect anything with the (Scrying) descriptor -- including Remote View. Likewise for other magic that targets or modifies the results of Scrying -- again, since Remote View has the (Scrying) descriptor. Of course, vise-versa for psionic powers that modify remote view, since Scrying has the (Scrying) descriptor.
Similarly, Knock would defeat Psionic Lock -- but Dispel Magic would not. (And conversely, Psionic Knock would defeat Arcane Lock, but Dispel Psionics would not.)
Magic Circle against Evil prevents mental control -- not specifically magical mental control -- so it would prevent Psionic Dominate from functioning just as it would prevent Dominate Person.
Powers that cause energy damage can be countered just as easily as spells -- they can't be counterspelled, but the energy damage itself can certainly be resisted.
I'm just not seeing the problem -- I skipped 2e, though, so I'm not familiar with that whole debate. Please, if someone could list some example problems from the XPH, I'd really appreciate it.
-- N