Recent apps isn't a list of apps that are still in memory, it's just a list of apps that have recently been running. Some of them may still be running, some may have stopped running but are still sitting in RAM, some may have been overwritten by other apps.
If you switch launchers, the launcher doesn't pick up the list from the previous launcher, it uses its own list and, at the time you switch to the new launcher, there are no apps that have recently been run by that launcher.
I don't know what you mean about them showing up in "AOSP recent apps". Recent apps is just a function of the launcher that's currently running. If you run a launcher that uses the same list as the previous launcher (which may be possible - I haven't tried every possible combination of every launcher), it would probably show the apps that had been run by the previous launcher.
But regardless of whether an app is shown in that list or not, it's not necessarily running. The apps that are running are the ones in the Active Applications list. And if you want to "clear" an app from memory and it's not on the recent apps list, just run it and close it. Running an app that's already running just brings it to the screen, and when you close it, it's closed. (It might still be in RAM after it's closed and you're no longer running it. If Android needs that space, it just uses it, even if the app is there. Even if the app is running - Android will just kill it. [SOMETHING has to be there - memory doesn't ever become "no value" - whether there's an app running there or it's just a bunch of bytes that used to be the app running there.] The memory manager in Android is pretty good. This isn't Windows, where you have to get as much free RAM as possible. In Android, unused RAM is wasted RAM [which is why app killers actually slow the phone down; they're a great idea - for Windows, not for Android].)
