Thermal parameters for the LM1117
I would take the lack of copper on the drawing for figure 6 as just being an error.

For layout 2 vs 12 there are two possibilities 


One is that measuring high thermal resistances is a bit of a pain and great accuracy is not to be expected. 
Copper is rather reflective in the far IR (and by reciprocity can be expected to have low emissivity), if they were running the thing hot enough to have significant cooling by radiation (Goes as the 4th power of absolute temperature) then it is quite likely that the bare FR4 is actually better then bare copper.


Junction to ambient often really means junction to heat transfer tab or pad (In other words, junction to infinite heatsink), you can probably confirm this from the derating curve and the junction temperature limit.