tranzor i think it would help if you read this entire thread that would answer the questions for you as i've pretty much documented my methods and any problems i've had fairly thoroughly
the deleted scenes came in two flavours on disc 2.
Workprint: good quality but not up to DVD standard, a lot of the sound fx was missing and only about half to three quarters of the scenes were intact
Betamax Transfer: horrible video quality but completely intact video and sound fx.
obviously i wanted to use as little of the beta footage as possible so i had to edit together the two different versions of the scenes to come up with an amalgamation which contained the best quality video/audio as possible.
after that the scenes needed to be deinterlaced (which is something i skipped on the original PAL version and caused me no end of problems with the conversion)
then of course bung them back into the main movie and add back any sound effects and then do all the usual stuff like syncing up the music applying fades etc. etc.
as long as you dont use any of the transitions or effects in womble it doesn't reencode anything just joins it all together into one movie based on the edits that have been made.
on the other hand if you are referring to the multi pass encoding that is because a VBR multi pass will always yield better results a CBR single pass. i want my edits to look and good as possible so im happy to deal with the slight extra inconvevience.
Version 2 (NTSC) is done but hasn't been torrented yet.
anyway hope that answers your questions