“Does that make sense?”
You're training a new employee in your group at work. You've just explained how to check an important spreadsheet. You're not sure if he understood your explanation, so you ask this.
Does that make sense?
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This question means "Do you understand?"
...so that's how to fill out a sales report. Does that make sense?
The question "Do you understand?" can sound very aggressive. We also ask "Do you understand?" when angrily giving someone orders. For example, a parent might punish their child this way:
A: You are grounded. No TV, no Internet, no phone for one week. Do you understand?
A: Do you understand?!
Because of that, "Do you understand?" has a bit of a hard sound. "Does that make sense?" is a softer way to ask if people understand something.