The risk is very much not the same. Running native code is much higher risk, compared to running JS inside a browser.
The list of bad things a web app can do is a strict subset of the list of bad things a native app can do (after all, the web browser is just another a native app).
While it is true, there are problems with customization and other features; a better sandboxed environment will be needed which e.g. can use command-line, better ability to control and make connections/interactions with other programs in the computer, locally storing file (even using without internet connections), etc. The web browser / HTML is, I think, not a very well designed sandboxed environment, really.