I'm sure they are doing that because they don't want to hold up the deliveries of all of the cars that people want to get upgraded to a P100DL until the new batteries are actually available in QTY. (Especially if they are already in the process of being shipped somewhere.)
But if the estimates on the site are accurate someone who orders a brand new P100DL could get it as early as next month.
So use their limited availability of the 100kWh packs, ~200 week, for new orders to push demand/delervies up, and then once demand for that falls they will use the 100kWh for upgrades. Once upgrades are mostly complete they will probably make the 100 kWh packs available for 100Ds. (I figure the timeline will be squishy depending on actual demand.)
I agree that is the reason they are likely doing it this way. When I read Tesla's reasoning, I too expected it to be like vandacca said that they'd just swap the battery prior to delivery and re-use the old pack as new - or for cars (like mine) not yet manufactured, simply swap at the factory. Their wording certainly suggested it: "Tesla customers who have ordered a P90D Ludicrous, but not taken delivery, can upgrade to the 100 kWh pack for $10,000. Existing P90D Ludicrous owners can also upgrade to a 100 kWh pack, but for $20,000, as their used 90 kWh pack will have to be recycled."
Tesla's wording suggested only the existing owners' packs needed to be recycled, but in fact it turns out many (all?) non-delivered upgrades will need recycling as well. This makes the apology at the end more appear more multi-faceted, though, they are probably apologizing to existing owners as well as new buyers whose Ludicrous Tesla dreams just went up in price... It is significantly more expensive to get into a top-of-the-line Tesla today. "While the P100D Ludicrous is obviously an expensive vehicle, we want to emphasize that every sale helps pay for the smaller and much more affordable Tesla Model 3 that is in development. Without customers willing to buy the expensive Model S and X..."
In a sense, there are three, maybe four levels of customers here:
1) the new/unconfirmed orders that can just click in their new selection and will likely get the pack first as the factory will simply source and build them that way
2) the confirmed P90DL customers with manufacturing and/or delivery still coming up, that have the option to upgrade at price similar to new order but will get theirs retrofitted a bit later (arguably good value for money still, because Tesla eats the recycling cost and you get a car to drive without delays)
3) the existing P90DL owners who can upgrade but at a significantly higher cost, this is still a privileged group as they are being catered to, but I can see how it might not seem that way compared to the previous groups
4) non-P90DL owners/buyers, who may have some upgrade paths down the road, but not yet - when 100D is widely available, I would expect 90D's to be replaced by it and existing ones getting a pack upgrade option (unless the 100 kWh pack is too costly to replace a mid-high-end model and they'll just keep the 90D)
The fact that, in the end, there even are customers in the second and third layers is exceptional in the annals of recent automotive history. The traditional retrofits offered by car manufacturers have been seriously limited in scope and mostly minor cosmetic and/or non-factory-install quality stuff. Tesla so far has had a different approach and, personally, with having had a P90DL (not yet manufactured) on order, the upgrade to P100D yesterday was a welcome option.
But I also understand there are shades of grey here and some understandable critique as well. The lack of model years (or even a secondary mid-year referesh point that some manufacturers have) combined with the delays in the manufacturing process, compounded by Tesla's international network for those of us abroad, certainly means increased risks for the buyer of not knowing how your new car will compare to the state-of-the-art when you get it.
It is, in reality, much easier to estimate this with other companies with clear demarkation lines. I mean, there are European Model X buyers who locked in their order in March (with a reservation made in e.g. 2013-2014) and are only getting their cars now. Many of these early adopters certainly went for the P90DL or maybe some didn't, but would have taken the plunge with a P100D... It would have been hard to estimate in March that this would happen.
However, again shades of grey, this is of course mitigated in part by Tesla's exceptional willingness at providing retrofits. So the good news is some of them can upgrade at price difference and all P90DL owners can upgrade. But for the guy who took delivery a few days prior, the price difference can sting of course, and for those who went with, say, the 90D for maximum range as advertised, the current retrofit options are non-existent (that can change down the line).
So, a complex question, certainly.
The P90D seems a little duplicative now. I would think they would just offer the (60D-75D)/90D/100DL now so they just have 3 models technically.
Judging by Tesla's launch history - unless the 90 pack remains for some cost reason, e.g. 100 pack is too expensive to make for anything but a special Ludicrous model - I would expect the 90D/P90D to fade out eventually in favour of a 60D/75D/100D/P100D line-up. Historically Tesla has kept some options for some time to appease both current buyers as well as part logistics. Once those hurdles are cleared, they'll likely clean up the line-up to whatever is their current new target for it.