Word templates were designed to work in Microsoft Word and only had to work in Microsoft Word. Any other editor that happens to support templates does so at the risk of Microsoft changing their proprietary format.
Markdown differs in this regard because it is an open standard, and can be written in any plaintext editor or even command line. Defining a template format would therefore be difficult because the features available in various editors will vary wildly.
Honestly I don’t see any need for this when you could just copy your “template” file and make changes as needed.
Additionally, editors such as Atom and Sublime text already have templating plugins which would make this redundant, and aren’t markdown-specific. There are also many template languages with varying degrees of features, which can be used to perform transformations on a text file to produce your populated template. Many of those tools can also be used via their own command line API.
That said, I don’t see any reason you can’t go ahead and add plugins to your favorite editor to handle templating markdown files specifically.