I certainly remember how it used to be possible to left-click through transparent HUDs in the past... Sometimes, LL changes the behaviour in their viewer without documenting it, and this got backported by me without even realizing it...
Anyway, for next release, the "AllowPickTransparent" debug setting will default to TRUE, and a new "Touch transparent objects" menu entry/toggle will reflect and allow to change this flag in the "Tools" menu of the viewer (below the "Pick..." entries/toggles).