Episode 2 of the restoration special confirms that Apple Corps Ltd have indeed found a film copy of "Penny Lane" with faded colours to restore for the new Beatles 1 collection. The films used to restore "Penny Lane" and "Something" are said to have come from an American collector, who had better copies than Apple had in their archives. Of course, when film archivist and restorer Ron Furmanek was taking stock of Apple's archives of promo films in the early nineties, he discovered there were lots of outtakes from the "Penny Lane" film, but the film itself wasn't there anymore. The version we have seen on TV in the nineties onwards have all been taken from a video tape they had of the film. This was the 2 inch tape from 1967, as originally televised on The Hollywood Palace TV show. Earlier, they often used to show a black and white copy on TV, at least here in Europe.
It could be that the American collector is Furmanek himself, who had in his collection an original 1967 35mm composite print with faded colours.
In comparing the video tape version (as seen in The Beatles Anthology, for instance), it looks like they haven't been able to fully restore the colours in the faded film they are now using. But I guess we just have to wait until it is released to be certain.
Had they asked me, I would have referred them to the Swedish Television company, where Peter Goldman, director of "Penny Lane" and "Strawberry Fields Forever" was working in the seventies. They have given us glimpses of a pristine copy of "Strawberry Fields Forever" on TV there occasionally, so chances are they also have a great "Penny Lane" in their archives. Could be that Goldman also had good copies of these films in his own collection. Born in Germany, Peter Goldman died in 2005, at 69.
As for the remastered sound on the music videos, it seems that Giles Martin have chosen the same approach as Furmanek did in the nineties, to use the mono mix as a template to create a new stereo image. The surround sound is said to just add "room" to the stereo mix.