We don't know what the 997 will offer in this regard. We're going to probably have to wait until the R-972 ships to get enough details (such as an owner's manual) to know those sorts of answers, I suspect.
The 990's "Upsample" mode can be used with any digital source (PCM, Dolby Digital, or DTS), although it prevents the use of matrix processing such as Pro Logic IIx under those circumstances. I don't know enough about Denon's AL24 or Onkyo's VLSC to know how that compares to them.