Not that we don't have enough of them already, but this release comes with a new port of the Doom1/2 engine as well[0]. I don't know either codebase enough to say what's different, but it's now C++ vs. the original's C[1], and appears to be some Xbox and PS3-specific code as well (not that it's useful to mere mortals)
Don't see how this re-release would have much effect on their value, given that the original games themselves have been "preserved" by many countless times over across the Internet, likely since Doom's launch. Not to say the disks are any less of a collector's item.
I was thinking that as the "new" versions make their way into the market the original versions might be harder to come by. But I agree, it's more about the physical disks with labeling than the content. I wish I still had the boxes.
[0] https://github.com/id-Software/DOOM-3-BFG/tree/master/doomcl...
[1] https://github.com/id-Software/DOOM