For our business, we use a mail handler to interpret and analyze emails to track stakeholder communications. The emails I send from eMClient are encoded with manual linebreaks and “=20”, “=09” and a few other strange characters. Our mail handler service is working with us to manually interpret these characters, but this is not ideal - it will omit legitimate uses of these phrases in the future as they are showing up as plaintext. 
There does not appear to be a way to prevent this from happening in the settings. We use GSuite Gmail as our mail processor.