You’re welcome!
You and yours enjoy a peaceful holiday season together 
I have not found saving eml versions in DEVONthink to work all that well. I much prefer the wysiwyg of a PDF. In Apple Mail, I select the email I want to save and select “Print.” In the print dialog, I choose from the drop-down at lower left the item, “Save PDF to DEVONthink 3”. The PDF that is saved to DEVONthink has the text layer intact. I do this all the time when I want to save receipts that include a software code, for example. Or a tracking number, etc. I can later open the saved version in DEVONthink and select and copy the software code or tracking number, etc.
I primarily store eml, and also export to PDF when required for some reason.
As you mentioned, a PDF can have some benefits over eml. But an eml also contains (header) data (perhaps @BLUEFROG can confirm), that might be required in the future for some reason. It probably depends what you want to use the email for I presume, like evidence in a legal setting perhaps.
Or to put it in another way: an eml can always be turned into a PDF, but a PDF cannot be turned into an eml unless the header data is somehow stored in the PDF.
Tip for DTTG users:
- you can also create a PDF from the iOS or iPadOS native Mail client by taking a screenshot and selecting ‘fullscreen’ at the top and share that PDF with DTTG
- you can import an eml by setting up split screen on iPadOS and dragging an email from Mail into DTTG
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