I had Save as … (encoding) commands in the main menu at a certain beta version, but some people (including me) found complicated, and even worse, deliberately chose a Save as … (encoding) command where they meant to reload with a correct encoding, and ruined existing files. That is why I hid these commands into the All Commands, but you can easily define your menus.
Unfortunately, Save as UTF-8 without BOM is not in a command list, but if you had EmEditor Professional, you would be able to write a simple JavaScript macro like this:
document.UnicodeSignature = false;
document.Save();
You would be able to assign this macro to a menu item, and insert the menu item to anywhere you would like.
Thanks for your nice comments!