That is expected behavior. It has existed even in MV2 (when I started coding extensions). If you want to detect when your Chrome Extension is enabled or disabled, then look for the chrome.management API, which requires the management permission in your manifest.
Note by adding this, your users will get the permissions warning: "Manage your apps, extensions, and themes" that they'll have to approve.
I believe the call you'll be wanting to intercept is chrome.management.onEnabled.addListener().