Hiya!! It is a bit of a generalization to say that France and all of its vassal fiefs were restricted to Salic law throughout the medieval period. The County of Flanders, the County of Toulouse, the County of Artois, and the duchy of Aquitaine had all been held by women throughout this period. Succession laws were by no means set in stone throughout the kingdom and many provinces had their own practices (the King wasn't unilaterally dictating succession practices and laws down to his subjects). There was also some give and take here if a succession crisis occurred as the law would be subject to interpretation (and politicking) from the King, the will of the local nobility, the church, and the deceased ruler's family. The County of Champagne had no prohibition on a woman inheriting the title, and Joan was able to maintain the support of the local nobility and the support of the French King Philip III, who betrothed her to his son in the hopes of gaining the county for the Crown.

As far as Salic law itself, this was an ancient legal code from the time of Clovis and it was not some kind of superseding law of the land, so there was no "adhered strictly to agnatic primogeniture" in principle. From 987 to the 1300s, the Kings of France had always passed the throne to their eldest living son without controversy or issue. This son was always the strongest candidate to be their heir by every measure (male line, proximity of blood and primogeniture), but there was no well-defined and organized law of succession should a crisis occur. This precedent fell apart however, when Louis X (Philip IV's son, so keep in mind this is after Joan of Navarre had already died) died with only a daughter of questionable parentage (the girl's mother had been accused of adultery) and a pregnant wife. His brother, who was regent during the period, organized a council of scholars, nobles, and churchmen who concluded that the throne of France could only be held by a man. This was not without controversy, and the regent (the future Philip V) had to negotiate with the Duke of Burgundy and other noblemen who would have supported the claim of his niece. The queen gave birth to John the Posthumous, who as you can guess, died in his infancy. Philip V also died without a son, so the throne passed to his brother Charles IV, who would also die without a son, but with a pregnant wife. Another council was called to determine what should happen if the queen gave birth to another daughter (which she did). The closest blood relative of Charles IV was his sister's son, Edward III of England, but the French nobility by and large balked at this. Instead, you get the strictest form of "Salic Law," that not only does a woman not have a right to a title, but that she does not even transfer that right to her sons. Therefore, Philip IV's line was considered extinct in the male line, and the throne would pass to Charles IV's senior-most agnatic cousin, Philip VI, the first Valois King (this decision would be the nominal cause for the conflicts of the Hundred Years' War). Technically however, since he did not descend from Joan of Navarre, Philip VI had no claim to Champagne and Navarre. Once again, however, he was able to negotiate, keeping Champagne in exchange for other territorial concessions, while Navarre itself passed on to another ruler (Louis X's daughter).

So as you can see, the definite nature of succession didn't really exist. The Valois Kings of France would themselves back a claimant descended from the female line during the Breton War of Succession several decades later in direct opposition to Salic Law. However, to strengthen their symbolic hold on the throne, they would later dictate that the appanage titles that they granted to their younger sons could only be held in the male line, mirroring the circumstances of their own succession. It's questionable the degree to which the Valois succession actually hinged on Salic Law, which would have been almost 800 years old by that point, being a creation of the Merovingian Frankish Kingdom. While it does provide a nice ancient legal grounding dating back to the times of the legendary Clovis, the circumstances establishing this succession dealt far more with the politics of the day rather than digging up a Merovingian era law that had been ignored, superseded, and negotiated many times by the 14th century.

To summarize, the laws of succession were by no means uniform and strict in nature during the medieval period. The principles of the Merovingian Salic Law offered a symbolic precedent for the later Valois Kings of France, but even their succession was dependent more on medieval feudal politics than ancient legal codes that long since fallen in use. However, since the succession disputes that resurrected "Salic Law" occur decades later, Joan of Navarre was able to succeed as Countess of Champagne without any serious legal issues. Let me know if you want any follow up or if you have any additional questions/want reading material!!