The 2004 and 2011 versions will probably not be included in future releases, and I'm fine with that. They'd be highly redundant anyway, as this new 4k version will probably redo most of the changes.
Ideally, we'll get preservations of both the '97 version (all they'd need to do is color-correct it) and the OOT as well from this new scan. One big question is whether it makes sense to use secondary sources for the vfx shots (those had faded beyond repair by the mid-90's) and splice those into the o-neg scans or if they should just use secondary sources for the entire thing so the difference won't be as jarring.