Well I don’t use Snappy Mail (tested the Rainloop integartion years ago), but I asume beside authentication there is still not much direct integration with Nextcloud. I also cannot speak for Nextcloud Mail, since I don’t use it either. You on the other hand seem to know pretty well what features are available in both apps. So if a feature you need isn’t available, you don’t have much of a choice but to open a feature request and hope that it will be implemented at some point in time.
At this point, the desktop client is probably the easiest option. Or you could connect Nextcloud as a network drive (WebDAV) to your computer and then upload the eml files through that. Uploading them via browser is of course also possible.