How do I Save Email using the Email Trigger to MSG format rather than eml format?

Not possible right now. You have to find a converter tool for that.

I am moving this topic to Feature requests.

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Can also change the folder created when the email is saved, it currently creates a number folder.

You can only change the base folder. But the numbering comes from the actual id of the email. We need to store them separately so that attachments do not overwrite each other.

What you can do is to use a file trigger to monitor base (and its sub folders) and then do whatever you want with the file as the email is saved.

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