Question: If both a lab and an assessment (for example) exist in a single QRDA file, with the same id root and extension, and a third entry's RelatedTo contains their common id, mood code, and class code, how could a receiving system know which element was meant to be referenced?

From Volume 2 of the HL7 QRDA-I Spec (Nov 2021 w/ Dec 22 errata) definition of RelatedTo, page 554 (emphasis added):

The id of the existing QDM element will be used to reference the already existing
data without repeating it in this template. The sdtc:actReference/id is required and must be the same
id as the entry/id it is referencing. The sdtc:actReference/id cannot be a null value. The
sdtc:actReference/classCode and sdtc:actReference/moodCode must be the same as the
entry/classCode and entry/moodCode of the entry being referenced.

RelatedTo elements use 3 items to link back to the referenced element: id, mood code, and class code.

But the Ensuring Data Uniqueness section of Volume 1 specifies that id is only required to be distinct per QDM type.

From page 50 of Volume 1 (emphasis added):

 

What makes data unique in a QRDA Category I file to ensure data is not treated as duplicate? The id element in a CDA template contains two elemental parts: a root (which must be a Globally Unique dentifier (GUID) or an OID25) and an optional extension (which can be any string of characters). If the extension is present, the combination of root plus extension must be globally unique.26 Identical id for an element refers to the same instance of an event. For example, two HbA1c lab tests for the same patient performed on different occurrences, each test is considered an instance of ["Laboratory Test, Performed": "HbA1c Laboratory Test"] and each must have a unique id, perhaps with slightly different extensions between the two ids (instances) if their roots are the same. Two entries in a QRDA Category I file from the same QDM data type with the identical ids are considered as duplicates.27

I understand the above to mean that two entries in the file could validly have the same id, as long as they are not the same QDM data type.

In such a case, if another entry's RelatedTo attribute referenced that (one shared) id, it seems we would need to fall back on the Mood Code and Class code to determine which element was intended as the referent.

But Mood-Class combinations are not unique per QDM. For example, class code OBS and mood code EVN are used by Laboratory Test Performed, Assessment Performed, and Patient Characteristic Payer, just to name a few.