But I'm talking about the anniversary. I think it'll be comprised of more than one episode.
The one they've only got 4-6 weeks to shoot in, in real 3D, which Moffat admits will slow things down. It takes them 2.5 weeks to shoot a regular 45 minute episode as it is.
And you're still assuming that they cannot
begin work months ahead of that 4 to 6 week span.
We know that they are shooting the hour episode which is to air on the anniversary itself in 3D. That doesn't in any way negate the possibility of additional anniversary episodes being made in the conventional way to air after the one that airs on the anniversary itself. Likewise, it doesn't negate the possibility that crews are already
at work on producing most of the parts of this multi-part anniversary story which don't actually require Matt Smith's presence, so that when he does become available, they can focus exclusively on shooting his scenes, as everything else will already be done.
Let us assume, for instance, that this anniversary "arc" story requires a number of lengthy flashbacks to The Doctor's early days on Earth. Such scenes could easily be shot by Gatiss, right now, concurrent to the footage he's already shooting for "An Adventure in Space and Time". Again, I'm talking about footage that would already be shot, and in the can, well before the official start date of the Anniversary shooting schedule, and wouldn't require any more shooting time than what you mention.