Leased the Prius Prime SE and drove it home.
I figured out what the $500 discrepancy was in the numbers that I posted above: missing dashcam. The deal was made when the car was supposed to include a port installed dashcam for $499, but for some reason the port didn’t install it and nobody noticed until I asked where is the dashcam. So I got it for $38.5k instead of $39k.
Also, the finance guys agreed to lower the money factor to the amount that TFS was offering: 0.00325. Shouldn’t make a difference with immediate payoff, but it’s one less thing to worry about.
I am happy with the deal, $5k over MSRP: $1k port option pkg + $2k dealer package + $2k dealer markup. It seems that most cars in my Gulf State area have a $1k+ port package, and most dealers here have mandatory $2k packages. Maybe I could have avoided some or all of that by shipping from another region for $1k but I never found that deal. I have been looking for a month with deposits at 5 dealers, and this was the first one I found. There are only 10 or so unaccounted Prius Primes in all of Texas at any given moment.
Also, ratefindr showed the $4500 lease incentive expiring around the end of this month for gulf states. Toyota will probably renew it, and other regions show it not ending until December, but a $4500 bird in hand has value.