The funny thing about this story, is that while at a glance it seems to give a straightforward skeleton of an answer as to whether this is really Doom and what happened to him... I say that the Doom Margaretta regenerated, and with whom she had been playing their game, was not the real thing.
Why? Simple: the *real* Doom wouldn't have let Latveria lie fallow, and under the likes of Tyger Wylde. And its clear that Latveria while the Doom that Margaretta was playing with was 'taken off the board' about ten years ago, far after Latveria was abandoned.
That aside, this story gave us what was probably the best Doom 2099 armor. Okay, it suffers from excessive spikes, and it looks too much like (relatively) regular clothing with armored bits, but the facemask made up for all of it.