Full AppleScript support would be amazing and my preferred solution on macOS! Since eM Client is also available on Windows it might be easier to offer a "Deep Link" Feature accessible via Hotkey in the meantime, which would alleviate most of the pain points IMHO.
Mimestream just updated their email app to support Hookmark and also SparkMail 3 (the new one, an Electron App) included a Deep Link feature (they are also cross platform).

Something akin to this (especially if it could work on mobile too with the same identifiers!): em-client://<UNIQUE MESSAGE ID> or even better with a second hotkey a markdown compatible format [Name of email](em-client://<UNIQUE MESSAGE ID>)

It is apparently better to use https:// universal links (at least on macOS), this is what the Mimestream team uses (https://mimestream.com/help/user-guide/deep-links).

This would make working with Task Managers like Todoist or Markdown based note systems like Obsidian possible!

Thanks!

The (popular Apple) accounting software GrandTotal sends invoice mails via AppleScript.
The following mail programs already support this: Airmail, Apple Mail, MailMate, Microsoft Entourage, Microsoft Outlook, Postbox, Sparrow & Thunderbird.

I, and I am sure many others, would be delighted if the eM Client could also be controlled and used via these programs.