Huh… I’ve installed 17 Casks; no apps have complained about being in ~/Applications. In fact, for properly written apps, it should not matter, so there may be something else going on.
I’ve been using ~/Applications forever for beta testing and accessing two different versions of the same app.
That's true. I hope more apps improve as well as OS X itself. The issue with ~/Application seems to be OS X-related as reported by HyperSwitch (http://bahoom.com/hyperswitch/), which cannot run in background without being under /Applications.
So that’s a HyperSwitch issue that doesn’t have anything to do the operating system itself. Properly written apps (and that probably means not using undocumented APIs or doing otherwise unsupported things) don’t care about being in ~/Applications.
I’ve been using ~/Applications forever for beta testing and accessing two different versions of the same app.