Really old thread but I was looking for this question and had to figure it out myself, but I found it.
The data for what is pinned and where is actually stored in the registry at:
Also it is still "Start8" in the path even if using Start11. Then the data seems to be stored in two places in different formats, in the "GroupContents" and "GroupContents11" keys/folders. The names of the groups seem to be defined in the "Groups" and "Groups11" keys/folders. I haven't figured out what determines which something goes into though - some stuff seems to appear in one or the other, while other stuff appears in both.
Though unfortunately for OP, manually adding items this way would be way harder than just pinning it the normal way. But it might be good to know if you want to manually go in and change the launch command for one of the shortcuts or something. Though even then, it would probably be easier to just make a shortcut using Windows how you want it, then pinning that.
Hope that helps anyone searching for this.