So, this happens cause now the updates site checks for updates on tool installers for all the updates centers configured in the system. Before this fix the tool installers updates were always checked against the default update center e.g. http://updates.jenkins-ci.org/updates/hudson.tasks.Maven.MavenInstaller.json.html?id=hudson.tasks.Maven.MavenInstaller&version=1.642.2-SNAPSHOT+%28private-02%2F08%2F2016+23%3A10+GMT-valentinaarmenise%29
Now, tools installers are checked against the update centers actually configured. If the experimental update center is the only one configured, there are no json files available for ant, maven and jdk (the tool installers). So we return the validation error, although the experimental update center has been successfully consulted for what concerns the plugins.
The error message is misleading, the problem is not the signature but the update json files for tool installers not being found. I could probably catch this case and avoid returning a validation error in case there are no json files for tool installers.
Only happens with the experimental update site, if it is accessed via HTTPS. Workarounds would be to not use one of these.