The preorder bonus for
Genpei Toumaden Sound Chronicle (also from SuperSweep) was a disc containing the stems from the new AQUA POLIS arrangement medley, which sounds a lot like what the notice on the SweepRecord page is getting at. If you consider "backing tracks" to be covered under stems, then there's other examples like
Battle Gear III and some MintJam albums. If you don't count off-vocal karaoke backing tracks, you're still right in that it's pretty rare for VGM.
As far as paying for a soundtrack and getting samples goes,
this Payday 2 release and its
"REMIX MATERIAL" tracks full of strung-together samples is the only other thing that springs to mind.
Then there's
Risk of Rain: Engineer Edition, but it was released as a separate purchase.
THQ and Sonic Foundry released a lot of samples from Toxic Grind as part of
a promotional remix contest for use in Acid, but these weren't available on
its soundtrack.