If Steam can still trivially get its third-party-bought programs onto the metro-styled start screen, the popular reporting on that situation was off.
And I can't even find a story where Gabe himself actually expresses an opinion on, or concern about, the MS App Store. His comments seem to entirely revolve around Metro being bad for desktop usability and Windows 8 not selling. So the popular reporting that Gabe was specifically upset about the store (via it's limitations) seems to have all been bullshit/editorial.
Upon digging deeper, it seems his concerns about Windows 8 aren't materially different than his comments about Vista (via complaints about DX10 being Vista-only, as Vista wasn't selling).
All mine are, by default. Valve is concerned about the competition from the Windows app store, not the UI revamp.
In my poking around on this, I saw plenty of assertions that this was all about the app store, but nothing is ever attributed to Newell except his lament that the usability is off and the sales aren't there.
But the 'doom and gloom', from Gabe's mouth, doesn't seem to be any more extreme than his stated position on DX10/Vista. As far as I can find, the press are the ones taking his comments to extremes, reading into them about app stores, etc.