Why is it "make sure that" (no 'it') but "make it so" (with 'it')?

Make sure is an intransitive verb in that context, that’s why. Your boss would not, I imagine, use its synonym, ensure, in that way and say Ensure it that . . .

I think the explanation is that "make sure" is a phrasal verb distinct from "make", and that the phrasal verb "make sure" can only take one complement, but that "make" can and frequently does take two complements (e.g., Make a boy a man; make yourself available).

Compare "make sure" with "make obvious":

Make it obvious that I won't talk to him.

is correct,

Make obvious that I won't talk to him.(*)

is not.

So it appears that "make obvious" is not a phrasal verb, and that when the verb "make" takes the complement "obvious" it must take another complement as well. Indeed, "Make sure!" and "Make certain!" are valid commands, but "Make obvious!"* and "Make available!"* are not.

As for "make it so", that one's a bit trickier. Is it (a) a set phrase, (b) the verb 'make' with the pro-adverb 'so' (similar to 'do it like so'), or (c) is 'make so' a distinct phrasal verb of its own?

If you believe (a), then you will simply say that 'it' is part of the set phrase and therefore need not teach any grammatical lesson. If you believe (b) or (c), then you need only explain that the verb construction requires a(nother) complement to be grammatical, just like "Make obvious!"* or "Make available!"*.

By the way, (a) may be undermined by the fact that it seems okay (?) to say things like "It was made so by the actions of the first king of France."

PS Notice another way to add a complement to "Make obvious": "Make obvious our objections to the decision."