Basically, stop thinking of Pym Particles as only dealing with size-changing. That they also manipulate strength and durability.
Something is definitely up with giant-man's durability, going giant shouldn't make you invulnerable but its usually shown as making the giant way more durable than a "regular" 50-foot man should be.
And somehow Ant-Man retains human-sized strength at small size. And sometimes retains human-sized weight, something he seems to be able to choose (in the books at least)
There is definitely a density thing going on with size changes. So from there its not hard to retcon Vison's density control, and being made by Ultron, to being some form of altered Pym process.
Now, I think the writer was stretching a bit trying to tie Wonder Man/Power Man's ionic powers into Pym particles. Vision's durability isn't anything like Simon's, Viz is just 100-tons of mass packed into a human shape.
And Vision isn't superstrong at all, not in the typical way of thinking of strength. He just shifts into super-dense form and then punches something with a 100 tons of mass behind the punch. He can't lift 100 tons when super-massive, he just throws his own weight around.
I'll give the writer some credit, i'm kinda surprised busiek didnt come up with his (he started during that Avengers/Thunderbolts crossover but didnt quite get all the way there). But I think you gotta retcon how Viz and Wondy work quite a bit before this axis reflects comic reality.
I expect eventually we'll retcon adamantium into having a Pym-related process, that the metal is so durable because it has super-dense properties while not being super-massive. More Pym Particle fuckery.