I'd like to see where it references that the Highwind is Mako-powered
It's not in the game, but in some official external sources I can't recall right now. There's even a mention of its Mako consumption rate...
the Sierra may just have a very large jet engine or some form of nuclear reactor onboard. Considering its extreme maneuverability and presumable increase in durability over the Highwind, I'd lean toward the latter option.
Nuclear reactors are hellishly heavy, due to the shielding and cooling systems... probably impractical for something like an airship, which depends on being very light.