PSO2 & PDf in the FY12 report on page 38. PSO under digital, Diva under packaged. Samurai & Dragon Vita was also listed under digital in the FY13Q1 report too, there's definitely a distinction being made.
PSO2 Vita is going to be both packaged and (free) digital, just like Samurai & Dragon Vita. And there's nothing I can find in any of IR docs that say they're combining package and digital in the platform breakdowns, indeed the SKU counts would imply that distinctly isn't the case.
edit: Quoted before your edit. The methodology for discerning the numbers is laid out by Sega in the notes. Quarters are cumulative, so Q2 contains SKUs & sales from Q1 added to it. You have to subtract 2 SKUs and 10k sales (Q2 lists 260k sales, not 250k). Sega also notes no catalog sales are included in the figures, it's only new titles and sales only for the quarter they release in.