The latest backer update has a section on this, which I’ll quote here to make things easier:
As we’ve mentioned before, all keyboards are shipping with QWERTY keycaps. Any extra keycap sets we owe you will ship later under separate cover. The factory says that the tooling for the packaging for the extra keycap sets has been completed, but we haven’t seen samples or photos of it yet.
The factory really doesn’t want to produce the ‘extra’ keycap sets until keyboard production is properly in hand.
To help control shipping costs and shorten timelines, we’re looking at shipping your keycaps to you directly from the factory. As we know more, we’ll definitely tell you.
When filling out the BackerKit survey, you should have had an option to buy extra keysets, including the runic one (Linear A), which will ship separately. I suppose the same keysets will be available later in the shop too.