If you intend on producing only a small number of copies I would suggest having a black (or some discreetly marked) frame at some random point. Vary this for each copy you sell/give out and keep a record of what marks correspond to what disc.
Disc 1: A blank frame @ 19281 - Sold to Mr. Charls F. Hillfongler
Disc 2: A blank frame @ 42212 - Sold to Mrs. Badface
Disc 1: A #21 in the top right of frame 15001 - Sold to Mr. Charls F. Hillfongler
Disc 2: A #56 in the lower left of frame 15001 - Sold to Mr. Badface
Disc 1: A red dot in the middle of frame 72144 - Sold to Charls F. Hillfongler
Disc 2: Pure black at frame number 3259 - Sold to Mr. Badface
That way, if you find a copy you can check for your mark and see which disc it was ripped from.
You could do a similar thing the audio track. Encoding the audio for each disc would be much than having to encode the video repeatedly, and would probably be more discreet.
Disc 1: A 500ms silence @ 00h30m21s024ms - Sold to Mr. Charls F. Hillfongler
Disc 2: A 250ms pop @ 00h47m07s965ms - Sold to Mr. Badface
Its allot of effort… so unless you are really worried about piracy I would just accept it as another overhead. While there was some (very limited) success burning a CSS protected DVD-R it is completely useless as a protection, has been for over 10 years. Even a complete novice can learn how to bypass it after a Google search and 5 minutes reading. Even newer commercial DVD protections have all been defeated, now with little more use effort than basic CSS.