It is clear: They are worried about "Submarine patents" popping up in the theora codec and being sued once they implement it.
However, remember that Apple is a MPEG LA member, so every time someone pays for H.264 license, a cut from the money goes to Apple.
For recent example why your theory of parity of exposure is not valid, see Microsoft vs. Alcatel-Lucent.
And what, pray tell, do you want me to take away from that?
My point is simply this: big companies know they can't avoid the possibility of patent trolls. The next best thing, then, is ensuring that your competitors in a given market are at least as screwed as you are if someone starts slinging lawsuits.
Having other people implement Theora first while they sit back and watch to see what happens gives Apple (and Nokia, which everybody still seems to forget) that position: if nobody sues immediately, they can choose to implement Theora and know they're no worse off than the competition. If somebody does sue immediately, they (Apple and Nokia) will just issue an "I told you so" and stay away from Theora.
Similarly, right now if somebody starts suing over submarine claims on H.264, Apple's not really any worse off than some of the other players.
This has nothing whatsoever to do with law or lawyers or courtrooms, and everything to do with managing risk.
"Similarly, right now if somebody starts suing over submarine claims on H.264, Apple's not really any worse off than some of the other players."
is simply not true. Microsoft properly licensed MP3 format. So did other companies. Lucent sued only Microsoft and not other companies. Patent holders can pick and choose who, when and where they will be suing for infringement. There is no duty to sue all known infringements.
But if you're the only company implementing the infringing technology, the risk is entirely yours. If lots of companies implement it, it's more of a game of Russian roulette; maybe they pick you, maybe not.
And historically, patent trolls don't seem to be quite so picky, and they're the ones to worry about. The Lucent suit demonstrates why it's so rare for bigger players to sue each other -- you end up with $BIGNUM suits and countersuits seeking damages which exceed the GDP of Switzerland, and that's not good for anyone involved.