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I think that currently it is not possible to update an mail, except for the flagged property.
Why don't you try to export the email and save it in a SharePoint List, with the generated ID as another column. Or save directly the bodyof the email to a SharePoint list (and saving the ID, too) ?
Hope it helps!
"The only possibility of editing an email I found, was flagging, but there is the only possibitity to make it flagged, not flagged or completed"
Please note if you manually flag an email, you can have a flow triggered "when an email is flagged', then execute whatever logic in your flow, and finally let flow mark this message as completed. Just guessing, your flow can convert the flagged email into .eml or .pdf format + send an email back adding a Unique ID in the Subject and a generic body ("your request is being processed. Keep this reference in the subject for future interactions bla bla bla") and attache the .eml / .pdf file.
I also considered to implement an automated ticket with Power Automate (aka Flow) some time ago, found similar issues as both you and @fchopo mentioned. We even planned to generate Unique IDs by means of an Outlook AddIn.
Hope this helps
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