LTI and Moodle

Another excellent question and one which will hopefully be resolved in LTI 2.1 which will introduce the ability to re-register with a tool provider.

In the meantime, with LTI 2.0, you have little choice but have multiple registrations with the same tool consumer if they want to add other tools.  You could try using the tc_profile_url or launch_presentation_return_url URLs (or at least their domains) to identify those coming from the same tool consumer.  Or, as you suggest, you may have given customers some form of key which allows them to identify themselves during the registration process.