Fortunately the originals are available, you can go out and get them right now as a matter of fact.
The problem is not whether they are available NOW, it's whether they continue to be available in the decades, if not centuries, to come.
I wouldn't at all expect a bluray release to branch between the two the way TOS-R does. The situations are entirely different as TNG's VFX shots will always remain SD, and there's no way to change that.
This isn't just the model work, you're talking about any scene with the view screen, transporter shot, hand phaser shots, Holodecks, window shots, hundreds of shots they produced over the years. Trying to mix all that in with newly restored and edited scenes in HD is neither practical nor does it preserve the 'original' episodes, as the discrepancy between the material would be massive.
And it DOES NOT MATTER how it's done, or how bad it looks; even if they have to keep the entire SD resolution episodes right next to the new HD ones. The originals need to be preserved, it's that simple.