re:I set up an auto-reply message with a PDF file as an attachment but it is sent in only plain text and decoded codes for the attachment and with this description: "This is a multi-part message in MIME format." as shown in the image.

But the image says : Content Type: text/html so it is not plain text, but it is not showing html, so I'm wondering if the email/template was created using html. Source code of email would show pdf attachment as per image.

re: Besides, I also set Send the message in HTML any way in the Composition section

I would always suggest you use the option 'Send the message in both plain text and html', so user has option.

Re: 'I set up an auto-reply message' I presume you created a 'Template' email.

Is the account set up so that when you click on 'Write' it offers the HTML option automatically ? You would see a 'Formatting Bar' in 'Write' window. Did you create that auto-reply message template email using a 'Write' window in Thunderbird and was it created using HTML or Plain Text ? Somehow, I think it was created in Plain Text, so no formatting is included.

I have set once plain text and then HTML only option for all the settings from the template itself and the current user to the global setting but no difference! Overall, The text is OK but the attachment is converted/decoded to letters as shown in the screenshot!

Yes by the Write option, I've created a template for an auto-reply message including only a sentence and a PDF file as an attachment and there is no HTML code at all.

Thank you for your time

This is an annoying problem and it is strange that there is no solution to this!