I.i.r.c. Chrome Apps are compiled binaries specific for Chrome (NaCL), they're more like Flash, Java or Webassembly applications.
Because of that, Google's suggested replacement of Android Apps (won't work everywhere Chrome does) or PWAs/Extensions (both heavily sandboxed) doesn't work.
There are javascript+html+css apps that could use the Chrome API ( https://developer.chrome.com/apps/api_index ) which allow them to do more than regular javascript+html+css web pages.
There is no compilation.
NaCl was supported in Chrome Apps, but most Chrome Apps are just web apps using the chrome.* APIs, not NaCl.