I'd probably try breeding them by just walling the male away somewhere, it doesn't matter if he goes feral. Don't know if dragonfire affects constructions (probably not, since magma doesn't), so that should be pretty easy unless you get really unlucky. Or you can do what I'd do, and make a raising bridge and mechanisms to link it out of
dragonfire-safe materials; easiest ones are probably nether-cap, only usable for the bridge, and dolomite/periclase for the mechanisms, or if those aren't available even by ordering from the caravan, adamantine. This allows you to seal the dragon inside, and it can't destroy the bridge. A line of cage traps along the only, winding (to limit LoS and dragonfire line of effect) exit. It seems you have most of the rest of the safety precautions pretty well worked out, and the dragonfire-safe materials aren't absolutely necessary, since a dragon won't flame if there's no target to do it at.
The real questions are: do they take any longer to hatch than say, domestic poultry? And it doesn't matter so much how long it takes a dragon to be fully grown, what matters is how long does it take to reach adolescent and be able to breed in turn (well, you can decide this when modding them to hatch)? In any case, once you have a couple of hatchlings, live up to the name of your fort, and have each entrance be covered by 1 or 2 dragon pillboxes. If you want, keep them constantly open behind fortifications, so all visitors will know that you don't mess about, when it comes to your name. I'm thinking of something like this:
D
WWFWW
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.....
WWFWW
D
Hopefully the only "friendly fire" casualties you'd get would be limited to whoever is passing through a relatively small portion of the corridor when the dragons fire on any kobolds they might notice. A small price to pay, for dragon-guarded entrances. For bonus points, make the fortifications out of clear glass.