I've never understood the appeal of distributing applications as opaque blobs that somewhat resemble dumbed down docker images. Using such form of distribution will unavoidably lead to bloat and make it very hard to even known what kind of code is actually used. It being such a trend with even a bunch of competing systems shows what kind of push the convenience crowd is able of, i think.
Considering the topic of abuse there should be little surprise here in my opinion. Giving people the ability to publish binary code to a large userbase with little to no safeguards in place is practically an invitation that screams "Hey mr. bad guy, please distribute malware!"... I still remember the concerns being raised when Ubuntu added their PPA system about how it would facilitate getting unsuspecting users to install bad software but in comparison to this app bundle trend it actually seems quite convoluted and ineffective.
I think if these app bundle systems keep up this easy distribution trend (which they probably will as convenience is their major selling point in my opinion) i wouldn't be surprised if at some point the old Windows tale of i-downloaded-this-exe-file-and-now-my-computer-is-displaying-popups-all-the-time will actually become a common thing on unixy systems too.