apt-get update incosistency

The 5th May result is not relevant. Not because it is for trusty and not xenial but in trusty you had enabled the repositories for the source code and also some PPAs as well as extras which are not enabled in the xenial installation.

I am guessing that the update utility has some way of knowing if a repository has had changes made to the software in the repository. If no changes have been made then there is no point is downloading the list of software in the repository to compare it with the software packages installed on the system to determine which specific packages can be upgraded.

This might or might not be a new thing for xenial. Certainly things have moved on for Apt in xenial. Although apt-get will still work it is now customary to use apt update and apt upgrade. You can check this out with the command man apt.

Regards