There's no difference between being the default for the desktop and being the default for Metro/Modern UI. There's only one place to set this, and it should cover both. You can however set only the extension .html to default to Chrome, and still have hyperlinks go to Internet Explorer.
It would not surprise me to find an entry in the registry that contradicts the default desktop program vs default metro, however there's no setting or place in the control panel to change this. Take a look at this question. The answer which received the bounty seems to indicate there is a registry entry somewhere that may or may not indicate an MUI app being set as default, however it may not have any effect on the behavior of hyperlinks.
Open up start and search for
Set your default programs:
Take a look at Chrome and see what it has set. Mine only had 3 out of 18:
There's a difference between .html extensions and HTTP protocol! Setting Chrome as the default for .html will cause .html files from the desktop or explorer to open in Chrome. We want to make sure that Chrome is the default for HTTP protocol.
HTTP, URL:HyperText Transfer Protocol and
HTTP, URL:HyperText Transfer Protocol with Privacy are both set.