So after speaking to support on both sides I am able to somewhat work around.
The host of the SMTP server tells me there is nothing erroneous in their logs or issues effecting my account/server and they have tested with various other email clients and have no such issues.
Support on EM Client have confirmed they also get the same issues as me, and after giving them a test account to diagnose further they indicate the SMTP host disconnects frequently and takes longer than 30 seconds to respond when it does work.
So while this isnt a solution and there is still a problem, there was one MAJOR breakthrough from the EM Client support which was how to extend the timeout for SMTP requests. To do this you can go to your account settings and then Advanced Options at the bottom of the page and in the Parameters field enter the following:
--smtp-timeout 3600 --smtp-initial-timeout 3600
I think 3600 here is the value in seconds, so we are saying wait 1 hour (60 seconds * 60), so you can set this to whatever interval you want, I have not done any in depth evaluation of the timeouts but I can see now that it is not erroring out as it did before, as the logs end with this now:
09:33:46.832|02E| SMTP S: 250 Accepted
09:33:46.832|02E| SMTP C: DATA
09:33:46.867|02E| SMTP S: 354 Enter message, ending with “.” on a line by itself
09:33:46.871|02E| SMTP C:
09:33:46.871|02E| SMTP C: .
09:34:16.945|02E| SMTP S: 250 OK id=1r665k-00GLOq-A1
09:34:16.947|02E| SMTP C: QUIT
It seemed to only take 30 seconds ironically to accept the email, but I could not find any information in the EM Client docs/articles about how to extend the timeout, so I hope this helps others solve/workaround the problem.