Pronunciation is identical.
Ali is fine for a small boy; I imagine it will naturally shorten/mature to
Al, if he needs a nn at all.
My son's 2nd mn is
Alastair. I would have preferred the
Alistair spelling, because I like the subtle repetition of a-i-a-i; however, the two friends we used the name because of both have the
Alastair spelling (and a former boyfriend of mine was an
Alistair!) so that's what we went with.
Of all your potential names, only
Theodora seems to stand out as different. Nice name, but in the wrong sibset.