It is confusing to users, especially new ones; they may not realise they need to copy the patch to the temporary area first, possibly even inadvertently modifying a patch in ways they did not intend to.
Adding to the confusion, changes saved through the “Save” button do not actually persist after it is turned off (this is a bug Gaia, although the Sound Designer seems to have found a way around it).
On top of that, editing patches other than the temporary one is just not very useful, because you can not hear what you’re doing. There are some scenarios imaginable, e.g. when you want to make a specific tweak in offline mode, or you don’t want to overwrite your current temporary patch. However these are exceptions to the rule.
The easiest is to just remove the Save button from all user patches. It can be replaced with an Edit button which copies the tone to the temporary patch. That should effectively prevent the user from shooting himself in the foot.
Ideally all edit fields would be disabled as well.
A means to directly edit and save patches outside the temporary patch can be reintroduced later (also for file patches), however that should show a warning to the user before continuing. This could be done as a menu option, or be offered as a choice after pressing the above mentioned Edit button. A separate feature request should probably be filed for that after this bug is fixed.