This suggests that they have ample parts for and have finalized the manufacturing/spot-welding/assembly process for the non-performance 90D drive train and control systems (and the fixed spoiler on the 90D), but perhaps have not done the same for a Model X variation without all the stuff that goes into the premium upgrades package. All of the Founders and Sigs had the premium package, so that means they could concentrate on a fairly small pool of options in order to produce all the Sigs and Founders cars. Maybe programming the robots to make an X without ventilated seats (and the necessary plumbing), without the LED accent lights and fog lights, and without the HEPA filter and dual-activated carbon filters was more difficult than just switching over to the 90D drive train so they could satisfy some early orders for those?
Or maybe it's a parts issue? If I had to speculate, I'd guess that it's the ventilated seats (or technically the non-ventilated seats) that are holding things up. Tesla brought the seat manufacturing in house for the X and the seats were known to be one of the factors behind the production delay. I'll bet they made a whole lot of the ventilated front seats (for Founders, Sigs and fully loaded P90Ds) but didn't anticipate high demand for the non-premium front seats among early production P90D reservations. So now they have to make a batch of those. Speculation, but certainly possible.
Good news for those who are waiting for 90Ds. Not so good for those waiting for P90Ds without the PUP. But like all things, this too shall pass...