While it makes sense that Microsoft is trying to move towards Javascript for Office Add-Ins to easily support the multiple platforms Office is now available for, there are some things that almost every platform has available that are not properly usable from a web browser.

For example, having access to native cryptographic functions is much better than using web-browser based cryptographic functions (for any number of reasons including security and performance). Some other examples include geolocation and file system access.

While it may be possible to simply build in an exception for things like native cryptography (which would be very useful) allowing for native hooks into the underlying system (obviously there would have to be a few trust boundaries) might also be helpful for allowing people to easily migrate their native Windows-only (or even Windows/OSX only) Add-Ins to the new model without having to rewrite their entire code-base in JS.