Youngster… 
That is very true. The legal rights on a Pand are derived from the legal rights that are registered on the Perceel. Which indeed will be specified in the notarized deed, or follow from the description of Onroerende Zaken and their ownership.
But the register in which that information is stored (Basisregistratie Kadaster, BRK) is not easily and automated accessible, for very good reasons. So if you need the link between Perceel and Pand, your best bet is still the spatial relationship, or a request for that information from Kadaster (which is not an option if you’re talking 4000 Panden or thereabouts throughout NL, which is the amount deal with in my daily work).
And yet: Even taking the legal rights into account, that does not explain some of the anomalies that are being published by the Locatieserver. Specifically this example, which I know very well since those parcels are owned by my employer, does not make any sense to me - and I have access to and have seen the actual deeds on those.
Kadaster is aware of the issue, as far as I know they are indeed working on it, but it is not a trivial task. I’m sure it will be anounced far and wide, including here, if such an administrative link would be available.