From MSDN Defining Document Compatibility
Document compatibility modes allow you to control the way Internet Explorer interprets and displays your webpage
Specifying IE=edge
instructs IE to use highest available engine for established and emerging industry standards.
For example in IE9 the highest version of the engine is 9 (likewise the highest version for IE8 is 8), but IE9 can also render a web page using the IE8, IE7 or IE5 engine (with all of their old bugs) and IE8 can also render pages as IE7 or IE5 did.
If you have a page that was designed for IE7 but a user is now using IE9 has the page breaks; rather than updating all the code to work with both engines one can add the <meta>
tag speficying that IE9 use the IE7 engine.
The Chrome frame recommendation is recommending this to future proof the code against new releases of IE. By specifying "use the latest version" you are not limiting the page to a specific version of IE.
In the context of your question I don't think that using Edge is specific to the GCF, but rather an instruction to IE.