I was testing Disjunction Shards from rogue's shady deals, and it seems that opposing save counts in bonus from spellcraft.
As these items are bombs (not even spell-like abilities), especially made against mages, this makes no sence.
Until further testing I can also speculate that with spell-flag, Protection from spells will also works against it, which means effective 15+ save against it for mages.The character also gains a +1 bonus for every 5 ranks in this skill to all saving throws against spells.
This seems to render whole point of these items introduced pointless.
I don't know about other shady deals items, because I haven't reach the proper level yet, but I expect all of them working in the same manner.