I think you are on to something with the Tiefling =
Alphatian idea, although they are an imperfect match
because 4E tieflings have strong fire connections
and Alphatians (at least those who came to dominate
the Alphatian Empire) have strong air connections.
Maybe we can use tiefling mechanics for Common
Alphatians of Cypri ancestry, firesoul genasi
mechanics for Flaems and Honor Islanders, and
a blend of stormsoul and windsoul genasi mechanics
for Pure Alphatians. Ochaleans would use the
mechanics of one of the other Cypri sub-races with
ability score adjustments more suited to clerics than
to wizards. We could complete the looting of the
genasi racial powers by assigning their remaining
manifestation powers to gnomes and aquatic races.
All in all, this is a much more satisfying solution
than my original idea of bringing the goatmen to
unprecedented prominence.
The dragonborn are much easier to account for, as
they were hiding in plain sight among the lizard men
of Mystara all along, with the 4E Monster Manual
giving us the one clue needed to find them. In the
4E MM, the main shtick of the lizardfolk is their
swamp walk ability, which makes them deadly foes
in their native swamps but virtually worthless
elsewhere. Whenever we find lizard men outside
of swamps, it is likely that they are actually dragonborn.
Note that this makes Mystaran dragonborn a hostile
race to the standard PC races, as they are more likely
to be found fighting alongside orcs than humans, but
viewed in this way they were present in the setting
from the beginning.