The way I see it, and trying to put myself in EJ's shoes, it is almost a dammed if you do dammed if you don't situation. The stage 2 upgrade is a worthy improvement but it is costly in parts and as important it is labor intensive. That is direct money outlay on EJ's part because he has to pay his employees.
He has stated that he very much prefers to do the stage 2 upgrades up front because the labor when upgrading. I can also see the negative about taking trade ins towards upgraded versions. They would then have "used" units that have to be sold as used. Of course there is also labor involved in refurbishing and cleaning these trade in units before they could be offered for sale (at a huge discount).
As I read in a review, they were facing a similar situation back when they had the original STP and offered the SE upgrade. They finally determined it would be better to just offer the STP-SE. At that time though the price premium between the two was not narrowly as large as with the stage 2 upgrade.
Hopefully I stated it clearly, and of course this is my view, not anything EJ has said to me. The only thing he has said is that the upgrade is expensive and very labor intensive.