The Terran Empire may've been "gung ho", but in the Prime universe the technology is still NEW
, and while they'd had 90 years experience with Warp 1 technology, humanity was still in its infancy with Warp technology, just like nowadays we are still in our infancy with nuclear technology. Sure we know more now about nuclear tech than we did in the 1940's, but it's still New
technology. And in Enterprise, sure Starfleet would've taken safety precautions, but they would not have been the same safety precautions that were in place 200 years later when the Defiant-class was launched, because Starfleet would have very little safety information to go on in the 2140's/2150's, compared to the 2370's. And dropping the engine into a seperate hull would've made more sense from both a health and safety perspective.