Unfortunately until Google adds Web Bluetooth support for Chrome on Windows you have to use the Native version.
The COM port stuff is a red herring - The Bluetooth LE UART never appears as a Windows COM port, so you won't see (or be able to connect) to it via the built-in windows COM port menus.
Espruino is a JavaScript interpreter for low-power Microcontrollers. This site is both a support community for Espruino and a place to share what you are working on.
Which IDE are you using? Are you using the normal 'web IDE' that you've used with serial devices before, or are you using the 'Native IDE' from http://www.espruino.com/Web+IDE#as-a-native-application ?
Unfortunately until Google adds Web Bluetooth support for Chrome on Windows you have to use the Native version.
The COM port stuff is a red herring - The Bluetooth LE UART never appears as a Windows COM port, so you won't see (or be able to connect) to it via the built-in windows COM port menus.