“Does it make sense?” or “Do you understand me?”?
"Do you get me?", "Do you get my point?", etc?
What is the courteous alternative of "Do you understand what I say?"?
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The courteous thing to do is always to portray yourself in a bad light. So don't run the risk of making the other person out to be unintelligent; portray yourself as unclear and let the other person contradict that.
"That's probably as clear as mud" is a customary expression indicating that you have not expressed yourself well. It gives your interlocutor the opportunity to agree (in which case they have not understood) or disagree (in which case you have expressed yourself well).
Other ways exist. "That sounded complicated!" perhaps; or "Did I explain that well?" Focus on what you said, not the other person's understanding of it.
Politeness really depends on how you speak, where you speak, who you speak with, etc. In any case, in addition to what you've mentioned, here are some more expressions: