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).