They were probably re-recorded also to make more consise, shorter versions, as all the original 12 Inches would've been too long to fit on one CD - although some tracks such as 'Shellshock', 'Sub-Culture', 'Perfect Kiss' and 'Hurt' were clipped a bit for Substance anyway. 'Confusion' is also in a different key (A flat minor, instead of D minor, if memory serves) probably to get a better vocal more suited to Barney's range. I read somewhere at the time that these re-recorded songs also featured in the 'Salvation' soundtrack, but as I ain't seen the film I don't know if this is true.
I like the Substance 'Temptation' best, but probably the original 12" of 'Confusion' a little better than the re-recording - which sounds much more dated now, possibly due to the 'digital' sound of the samples and synthesizer sounds, rather than the analogue sounds in the original.
Wouldn't have thought they've mastered them from vinyl somehow - Substance only came out six years after 'Ceremony', so it would take some serious disorganization to lose or damage the master tapes. Then again, this was Factory Records...
Andy.