Very often when a person describes his point he asks the audience a question.
Does it make sense?
Is it correct to rephrase it as “Is it understandable?”
Rather than does it make sense or is it understandable, I’d use that (where that refers to what you’ve just explained.) Using it here is common among native speakers, but not idiomatic.
Otherwise the two do mean the same thing in this context, yes! “Does that make sense?” or “Does everybody get that?” would be common things to say in this context, and they do essentially mean “Was what I just said understandable?”