Posting the solution that worked for me in case it can help anyone else, sorry it's so late.
The most reliable way I found for doing this was to include the attachment as base64 in the eml file itself, bellow is an example of the eml contents.
Note 01 : the base64 for the file comes from running the base64 command on linux using the attachment as an argument (should work with any base64 tool)
Note 02 : the string used for the boundary is just nonsense using the date and random upper case letters
Filename : emlfile.eml
From: Sender <email@example.com>
Subject: Generic Subject
Content-Type: multipart/mixed; boundary="19032019ABCDE"
Content-Type: text/plain; charset="US-ASCII"
Generic Body Copy
Content-Disposition: attachment; filename="MyPdfAttachment.pdf"
*base64 string goes here (no asterix)*
Then the filename.eml file can be sent using the command and it will include the attachment
# /usr/sbin/sendmail -t < filename.eml