This is one of the wrinkles of the federal structure of the German education (and research) system. Since the universities are run by the federal states, they are covered by the TV-L (Tarifvertrag für den öffentlichen Dienst der Länder, payment agreement for the public sector of the states), while institutes run directly by the federal government (e.g., the Max-Planck institutes) are covered by the TVöD (Tarifvertrag öffentlicher Dienst, payment agreement of the public sector). (Before 2006, this was the umbrella agreement for (almost) every public sector position, but then the states split off from the negotations; after the TVöD was successfully negotiated, they did not (could not?) rejoin and negotiated their own version based on the TVöD agreement.)
The differences are minor to the point where they should not be relevant in practice; in particular, the difference in pay scales within the TV-L for the different states is larger than the difference to those within the TVöD. The only possible point is that they are different agreements and therefore negotiated independently (with the same union, though), so a new round of negotiations might be completed earlier for one than the other.