Yeah, as you say anything fed from a control panel isn't part of the electrical installation for CoC purposes, only the main power distribution DB's and sub DB's plus the final circuits to the point of isolation.
Is there a back-up power solution ie generator/UPS etc connected to the baggage handling system? If there is it makes your life fairly easy. Back-up power would also be a double-edged sword because if there isn't any then it's going to be kinda difficult to motivate it as a critical system and get it considered for any special treatment or exemptions.
TBH if the rest of the installation is compliant plus there's no socket circuits then I would seriously consider just issuing the CoC with a calculated IR result and leave out any off-load voltage results you can't obtain and include your reasons in the notes section.
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