If you receive the email and click the reply button for the email you will see it does correctly reply to the address the user submitted because we use the user supplied email for the "replyto" address.
The problem with using the user entered email as the "from" address (as we once did) is it can make the email look like spam. Many spam filters will check that the from address corresponds to the DNS mx record for the domain of the from address. If it does not match it can flag the message as spam. Spoofing the from address is the most common indicator of spam. In fact some email providers will not let you send mail if the from address does not match the email account being used to send the mail.
So generally all email from the site should be from the same email account used to send email, so the site settings from address should be the same address as the smtp user email account. The "replyto" address can be different than the from address and works as expected without any spam blocking issues.
Hope it helps,