Chromium vs Android
There are a couple reasons why we open activities launched from Chrome with NEW_TASK flag. The biggest reason is that it provides a much clearer user experience: the user sees the new app as a separate entry in recents -- also, if we were to place a different application on top of Chrome activity, the Chrome icon may end up opening that application sitting on top of Chrome, which is fairly confusing for the user.
-- Bug 445956, wherein the Chromium developers consider the Android task metaphor too confusing for users and work around it.