Mismatched signatures have been discouraged since day one of Android. A mismatched signature is a sign that some one other than the original publisher built this package, and the user needs to be aware that it might be malicious.
That F-Droid went with this setup with mismatched signatures was always going to make their apks look suspicious.
It's a problem of trust. Differing signature is an indication of third party tampering. People shouldn't start to see difference in signatures as an ordinary occurrence. It should be an high alert event.