Hello, Gemma
Thank you for your question.
Let me start from the basics. By design, any email has 2 From addresses: regular From, and so-called Envelope-From that may be different addresses.
Every bounce-back email goes to the Envelope-From address and specifying the Reply-To address will not override this configuration.
Microsoft Dynamics 365 Marketing product by default is configured in the way that the system will get and process all bounce-backs you may receive on your behalf.
This is done by adding a special unique email address, for each email you send, to the Envelope-From header of that email.
Based on your specific domain configuration, this address is either using Microsoft-owned domain, or the domain aligned to your Authenticated From domain, if you have configured Custom Envelope-From address.
Second part related to the Out of office replies. Automated responses will not go to Reply-To address by the way this feature is designed.
More information on the topic you may find in our documentation: Troubleshoot email forwarding and replies
