If you open your EDMX model, you can right click and choose "Add code generation item"
This will add a T4 template to your project (which is the same as the default template of your EDMX model). If you take a look at the code behind this template, you will find the comments. You can just remove them and save the template and your code will be generated without the comments.
The part you refer to actually looks like this in the template
//------------------------------------------------------------------------------
// <auto-generated>
// <#=GetResourceString("Template_GeneratedCodeCommentLine1")#>
//
// <#=GetResourceString("Template_GeneratedCodeCommentLine2")#>
// <#=GetResourceString("Template_GeneratedCodeCommentLine3")#>
// </auto-generated>
//------------------------------------------------------------------------------