I remember years ago asking- let's say a general motor manufacturer- why truck manufacturers were going away from manual transmissions. The main reason was lack of demand, but there was another not insignificant reason- development cost. Specifically, the cost of EPA powertrain certifications. Apparently, the EPA requires every possible vehicle powertrain configuration to be emissions certified through them, and any possible changes or variations of a vehicle's powertrain (be it engine, transmission, drive wheel configuration, etc) require an extremely costly EPA recertification. If that's true, then it's entirely possible and believable that the EPA would make GDE recertify their tune for any and all changes to it. And given the way diesel emissions are currently regulated (almost as if the EPA is trying to kill diesels and push everyone to "clean" battery electric vehicles), I'd say it's more than likely.
The good news is that GDE has an engine brake option- other tuners aren't even interested in trying to offer that. While it's not cheap (~$1000 if you don't keep the flash tool), it's cheaper than trying to create your own engine brake option.