Answer
This is supported natively: upload each company's logo as a separate image through the 'Report Images' form in the Aurena client, giving each uploaded image a distinct, identifiable name (so you can tell which image belongs to which company). Then, on each individual Company record, set the 'Document logotype' field to the correct image name for that company. This gives each company its own correctly-matched logo on reports without needing any workaround — the standard functionality already supports per-company logo assignment this way, it's just driven by image naming and the per-company field rather than a single shared setting.