DT nipples simply extend the threaded, cylindrical section towards the hub as you buy longer nipples. If you're 3 mm short @ 12mm nipples, building with 14mm should bridge the gap nicely.
(pic off an earlier post somewhere)
I'm not entirely convinced about how bad it actually is to use longer nipples to compensate for short spokes.
It's not like the spoke/nipple interface can know if you're using a longer nipple b/c of inventory reasons, or b/c the rim profile requires it to provide tool flat protrusion. And then choose to fail or not depending on that.
If there really was a risk to it, shouldn't there be a disclaimer notice about building with longer nipples regardless of cause?
Looking at the pic, it seems to be about 3 turns from start of nipple head to the available full thread engagement for the 16 mm spokes. You'd need a very accurate build to get that. Particularly considering that spokes are usually sold in 2 mm intervals. And then you're maxed out on available spoke tension.
THAT sounds like a sketchy, impractical build.
And of course, there's the big variation in number of spokes, type of hub, rider weight, riding style etc.
I had a Chimo road bike with a 6-speed rear, 36-spoke that had threads showing above the nipple on the NDS.
For the kind of use that bike got, that was apparently entirely sufficient.
I went through at least two freewheels w/ any spoke issues before the bike got passed on for other reasons.