But the one who joins himself to the Lord is one spirit with Him. In an attempt to motivate believers to live righteously in light of who they are, Paul invokes the most intimate description of the marriage relationship. Paul describes the relationship of Jesus to the church as a Husband to a wife. For this cause shall a man leave his father and mother, and shall be joined unto his wife, and they two shall be one flesh. No matter how many times you read this scripture that is exactly what it says.
Many commentaries agree.
When Paul uses the word mystery is does not mean something which cannot be understood. But this is never the meaning of the word in the New Testament. It means there some doctrine or fact which has been concealed, or which has not before been fully revealed, or which has been set forth only by figures and symbols. When the doctrine is made known, it may be as clear and plain as any other. What a wonder.