Substitute one word for the italicised expression.
He did not make perfectly clear what was meant by a significant submission.

The phrase "did not make perfectly clear" means the speaker left the matter vague or difficult to understand.
Obscure means to make unclear, vague, or difficult to see/understand, which perfectly fits the contextual usage of failing to make something clear.

Mystify means to utterly bewilder or perplex.

Conceal means to hide.

Elucidate means to make clear or explain (which would be the opposite of the given negative action).

Therefore, obscure is the most appropriate word to substitute the italicised expression.