I just started using eM Client today (thinking of replacing Mozilla Thunderbird because it keeps freezing up intermittently for unknown reasons) and so far, I’m pleasantly surprised. I’m especially excited that you’re working on a Mac version and I downloaded the beta to experiment with on my MacBook Pro. The Windows version of the program is, for the most part, well-written, uncluttered, aesthetically pleasing, fast, and trouble-free. I like how there are so many interface settings such as the ability to hide local folders and to customize the toolbars. I really like that you can print directly to PDF, and the resulting PDF files remain text-searchable and preserve the hyperlinks in the original email. However, I have exactly the same two problems as David:
(1) Save as PDF defaults to the last File - Save As (*.EML) folder, rather than letting you set a default folder.
(2) Save as PDF always saves the file as “message.PDF”, rather than letting you use a renaming template.
I didn’t realize Print - Save as PDF was defaulting to the last File - Save As, and since I never use EML files, that was a good work-around for me: I saved an email as an EML file only once, to the Desktop, just to change the Print - Save as PDF default to the Desktop. Still, there should be settings to change the default Save as locations (one location setting for File - Save As and another location setting for Print - Save as PDF).
The second problem, always saving as “message.PDF”, is annoying in that it will cause you to repeatedly overwrite the already-saved message.PDF if you’re not paying attention.
If the software authors can implement these two changes, I’d suggest using renaming templates similar to what you see in CoolUtils Total Thunderbird Converter. In TTC, you can set a default folder to always save the PDFs into, and you can set an automatic renaming string such as [date] - [subject] to automatically rename one or more emails when converted to PDF:
2018-11-22 - Thanksgiving photos.PDF
2018-11-23 - Bank statement.PDF
The [date] uses ISO 8601 international date format so that the resulting PDF files stay in chronological order.
For more granularity so that every email is guaranteed a unique name, you can modify the renaming string to use hours, minutes, and seconds, or to use the message counter (email number):
2018-11-24-06h07m08s - Invitation, RSVP
2018-11-24 - Invitation, RSVP - 
A third feature which would be amazing and would instantly make eM Client fiercely competitive with Total Thunderbird Converter would be to allow the user to save multiple emails as separate PDF files. Currently, you have Tools - Settings - Print - Checkbox for “Print each mail on a separate page”. Why not another checkbox for “Print each mail as a separate PDF”? Of course, to do this would require some kind of automatic renaming as previously mentioned, to keep the files generated from overwriting each other.