I agree, the holy site placement is problematic, though not something that cannot be overcome. Romuva and Zunism are both small pagan religions, and while some of their holy sites are within one kingdom or at its border (Romuva has two holy sites in Lithuania and a third one right next to it, while Zunists already own one holy site and a second one is right next to them), both religions have holy sites that are distant or very hard to conquer: Zunist holy sites in Cairo, Nishapur and Multan are controlled by either the Abbasids or one of their tributaries, making conquering the provinces quite challenging; and Romuva's last two holy sites are in Bryansk (quite deep in Russia), and Rana (in Pomerania), though neither are that hard to gain access to.
In addition, in the mod When the World Stopped Making Sense, which includes Vasconic paganism, the holy sites are placed somewhat like Romuva, with three holy sites near Navarra and the last two further away: the holy sites are in Navarra (d_navarra, k_navarra), Asturias de Santillana (d_castile, k_castile/asturias), Toulouse (d_toulouse, k_aquitaine), Cadiz (d_seville, k_andalusia) and Roma (d_latium, k_romagna).
Finally, it is worth noting that while thee Basque were during the Middle Ages limited to the region around the Bay of Biscay, during earlier periods of time they were spread much further in Gascony and Iberia, so if push comes to shove, holy sites could be introduced to provinces which haven't had Basque presence since the Roman era. So with this in mind, I would probably place the holy sites a bit like this: one in Navarra (either Viscaya, Nájera or Navarra), another relatively close, either in Iberia or Aquitaine; third one a bit further away in the region that wasn't chosen: and the last two in some distant location in Iberia and Western Europe, respectively.
And yeah, Vasconic paganism would be partially balanced by its difficult starting position, either lodged between Francia and the Umayyads, or France and the Spanish kingdoms. An independent pagan Basque realm could wind up easily holy-warred into oblivion, much like Zunists.
Province culture and religion are meant to represent the culture and religion of a given region's population and peasantry; not the culture and religion of the nobility who rule over the region. Do also remember that the rural population does usually make up the majority of a given region's population: especially in Navarra, which wasn't a particularly urbanized region during the Middle Ages. As such, the Christian nobility and city dwellers would probably be the minority in comparison to the pagan rural population, especially given how there weren't serious attempts to convert the rural population until the 10th-11th century, and even then, the pagan communities persisted for centuries. So to summarise: no, Vasconic paganism would perfectly fit on the map. The situation would probably be best represented by having Christian Basque rulers govern over pagan provinces, and giving Vasconic pagan provinces "hard to convert" modifier, similar to Romuva and Bön.
And yes, while courtiers are primarily meant to represent the nobility and the upper echelon of a given region's society, they can represent any noteworthy character interacting with the rulers, and as such, courtiers aren't all necessarely members of the nobility, as there are several ways for lowborn characters to become members of the court in-game, be it via events or being generated randomly over time. I also want to point out that there's a mention of a Basque warrior called "Saltan, knight of the pagans" in Umayyad sources, so I think it wouldn't be that big of a stretch to assume that notable rural community leaders and pagan warriors could've become part of the Christian Basque rulers' courts.
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