The first time I saw Best of Both Worlds was the feature length VHS release and I thought it was edited together quite well, going straight from Riker saying 'Fire' to the shot of the deflector dish firing, the music blended quite well too.
If they are using the same edit then it would explain why the commentary can't be cut up over the season sets as there is a good 7-8 seconds missing from the feature length version.
Oh and for those in the UK the BoBW disc is only £6.99 at Sainsburys
I wonder if they will include a discount voucher in with BoBW for TNG S3 or S4 like they did with the sampler which had a voucher for £5 off TNG S1