I've not actually seen the old Doctor Who programmes (started with Eccleston), but did they not show him regenerating into whoever came next? I assume he must have looked alot younger back then, so if they showed the younger version of him regenerating wouldn't that make his appearance in the new episode a continuity error?
My understanding from what was said on screen was that Tom Baker was playing a version of the Doctor from Matt Smiths versions future. There's a line where he says something along the lines of 'trying an old face on again'. The implication I took from that was to mean that this was a future Doctor, hence no continuity errors.
Either way I thoroughly enjoyed the special episode 'twas a brilliant story and really well done with loads of lovely moments. Two things I liked: The way they used Billie Piper without bringing back Rose and that they ended David Tennant's appearance with the same line he used in his last appearance as a series regular 'I don't want to go'.