The difference is that you’re probably loosing information when you convert a rendered eml file into PDF. E-mail messages contain much more information than what is usually visible.and that information might be required under certain circumstances.There might be legal reasons to prefer eml for example.
You can convert eml files into PDF multiple times but you (probably) cannot reverse that process, unless the eml is somehow part of the PDF metadata perhaps.
If you setup a mail rule on macOS mail, you might be able to have it automatically import flagged e-mail for example into DT and subsequently have the rule unflag it.
Or as an alternative automatically backup each e-mail into DT and process them there or in DTTG after synchronization. If you use this script on macOS, imported emails are assigned a message URL that works across macOS and iOS as long as you setup that mail account both on macOS mail and the iOS Mail app. That way, when you (re)view e-mail on either DT or DTTG, you can open the corresponding e-mail in macOS or iOS Mail with one click in DT(TG).