"To come over" is only used to refer to your house or place that you are residing. It could also be the place that you are currently at (an office, desk, etc) "Do you want to come over" is asking the person if they want to come to your house or to the place that you are to either spend time together or often help you with something. "Can you come over and help me with this" (sitting at a desk).
"To come" can infer "to come over" if you already establish that you are leaving to go home. "I'm going home. Do you want to come?" You could also say, "I'm going to a baseball game. Do you want to come?" However, you cannot say, "I'm going to a baseball game. Do you want to come over?"
Exact same meaning:
"I'm going home. Do you want to come/come over?"
"Can you come/come over and help me with this at my desk?
"I'm going to a baseball game. Do you want to come?" (You can't use come over here)
"Do you want to come get some coffee with us?" (If you say, "Do you want to come over and get some coffee with us," you're probably asking if they want to meet at your house before you all leave to go get coffee.)
In conclusion, use "come over" when you're referring to your place of residence or position that you are (optional), otherwise use "to come."
Hope this helps! Best of luck!