i.e if item-level_itypes is on "bibio record" and if you have in items.itype an item type you want to delete via itemtypes.pl you can't do that. And you can't change this via the interface. The better way would be that Koha do check only in the good table depending on the system preference to allow the delete. I will check if it is also in master. I will propose a patch. Thx.
Christophe did you find that this bug exists in master? If so please update this bug report's version information.