Last week, I started to look at MDL-64786 which should bring the ability to explicitly rename the prediction models. They should still default to the associated target's name.
We also had a good discussion over the proposed implementation of MDL-61667 and MDL-64777. Particularly, we were talking about the expected behaviour in cases when the in-built models are removed and whether or not they should be automatically re-created etc. Luckily we concluded what I believe is really elegant solution. So that models declared via the db/analytics.php will be re-checked on upgrade (as they are in the current patch), but the declared indicators will not be taken into account when checking if the model is missing or not. In other words - if the admin replaces the in-built model with a custom one aiming the same target, Moodle will not insist on having the original model restored during the upgrade. As long as there is some model with the given target, the in-built model will not be auto-restored. On other hand, when restoring the in-built models explicitly (via the new button), admins will be given a list of defined models and they will be able to selectively choose the ones to restore.
This week, I am about to implement the received peer-review feedback and continue with MDL-64786.