Is the parents' refusal to allow their son to marry a girl—because she does not agree to the family house system and shared meals—considered an injustice to the girl, and must the son obey his parents in this refusal?

Your family does not have the right to prevent you from marrying, nor are you obligated to obey them in their condition that your wife live with them; for a wife has the right to an independent dwelling. Strive to convince your family, and seek mediation through some righteous people. If they do not agree, there is no sin upon you in marrying without their consent. However, it is preferable to leave her and search for another if you will not be harmed thereby.