Various troubles when an application is registered as installed twice in the same namespace with different versions in Extension Manager

We got the following issue when upgrading test.xwiki.org (from 12.6.4 to 12.10.5): I first upgraded the wiki to 12.10.5 by using the DW without any issue. Then I performed a "Check update" in Administration > Extension > Updater, where I saw that Application Logging could be updated from 12.6.4 to 12.10.4
I found that weird to not be proposed to upgrade it to 12.10.5 (see step1 screenshot). So I went to Extension Manager to check which Logging Application extension was installed and I found that both 12.6.4 and 12.10.5 were installed (see step2 screenshot). I then checked the available extensions for Logging Applications, and I saw that it was proposing to install either version 12.10.5 or 13.1 (see step3 screenshot). I tried to install 12.10.5 and got an error saying 12.10.5 was already installed (step4 screenshot). Then I uninstalled the 12.6.4 extension version. When checking back in EM the available extensions, it was still displaying both versions 12.10.5 and 13.1 (step5 screenshot).

So the bug is probably that somehow someone managed to install two versions of the same extensions which should not be allowed IMO.
tmortagne managed to find that there was previously both 12.6.4 and 11.10.2 installed:

as to why there was two... in theory the only ways are:

• manual filesystem modifications (I doubt it)
• someone imported a different version than the installed one at some point
• some bug during 12.6.4 upgrade that was not noticed
• having two competing versions in that wiki is actually much older (and most probably caused by an import) and nobody noticed it in all the previous upgrades (there was no real reason to notice it)