1. Timing and A/F are two completely different animals
2. The SVT 2.5L PCM calibrations are written for a 2.5L 10:1 or 10.25:1 CR (depending on year, yadda yadda) high output engine (read as aggressive timing and A/F ratio, ie as far as you can safely go for that CR)
3. The Taurus 3L PCM calibrations are written for a 3.0L 10:1 CR normal output engine (read as less agressive timing and maybe A/F ratio)
Now, if you combine #2 w/ a 3L w/ a 11:1 or higher CR, you have a recipe for detonation. Sometimes it doesn't happen, sometimes the knock sensor makes the ill effects less apparent. But detonation is still going to be a major concern in this situation. Let's see, an 11+:1 CR, an overly small combustion chamber for the engine bore (ie leaves overhangs into the bore w/ much more likely hood of hot spots which can propogate detonation regardless of timing advance) AND a timing map that is aggresive even for a 10:1 CR engine is asking for serious trouble w/ regards to detonation issues. I'm glad to hear David Z hasn't had any problems (especially considering the crap that California is pushing as premium fuel

) though I am sort of surprised that he hasn't.
The reasons I would suggest the 3L PCM over the stock SVT PCM is a less agressive timing map, more suited to an even higher compression engine, and the algorithms in the 3L PCM are written to take into account the larger displacement of the 3L.
Personally, I would use whatever PCM I had, and have a chip custom-burned for my application, on a dyno if at all possible. This will aleviate any issues w/ either PCM, and provide the optimum safe tune (provided you have a good tuner) for your combination.
Another couple of points I want to bring up, because some may not be completely clear on them.
1. The Apexi can only alter the A/F ratio, and has no control over ignition timing.
2. Ignition timing, if set too agressive for a particular application WILL cause detonation.
3. An overly rich A/F can kinda almost compensate for a borderline detonation situation, hence the stock richness at WOT on the SVT PCM (ie, the timing is set about as far as it can go w/ out problems)
4. Aside from pouring a can full of metal shavings into your engine, detonation is THE fastest way to destroy an otherwise very nice motor. The forces that come with detonation are such that they can destroy even the strongest of engine components (I have seen plenty of holed pistons and broken con rods and even cracked heads and blocks to attest to this fact)