I've never heard of PCM being a standard either. I always thought that some form of DD (2.0, 1.0, etc.) was the minimum standard for all dvd's.

What if the "spot" is from the laserdisc material itself?
Then it is a spot which came from the master and will be on all three captures, thus ending up on the output video. In this case, like noise, it will go through filters that will remove most of it, if not remove it completely. Spots like that are much less noticable during playback than big rainbowy laser rot spots.

Also, will you be encoding progressive, or interlaced ?

Progressive. Don't question it!