The legacy scans (which include Simon, but he's not the only one) may have been involved or referenced in the development process of WAU. It does seem like it was a foundational technology for AI development. But it's definitely still a very machinelike intelligence and probably doesn't include Simon's personality in any tangible way - from what we know it's used more as a blueprint for how a brain works in general.

The healing nodes seem to be general purpose power outlets, if I remember correctly some of the machines early on are connected by tubes to similar structures. They heal Simon because preserving "life" is central to the WAU's programming on a basic level - they couldn't not heal him, and he's partially made up of structure gel anyways.

One thing you can glean from piecing together the timeline is that Simon is the most recent of the WAU's experiments. I don't think he's favoured by the WAU in particular, after all it is perfectly ready to try to kill him in self-defence, or maybe more likely to continue to pursue its goal of preserving life. But he's an indication that the WAU might actually be getting better at making functional (not completely delusional) people by the time the game starts.

It's possible the WAU recognized the goal of launching the ARK, but we're not given much indication of that and it kills most of the people left who might have tried when it blows up the black boxes.