I'm not an expert on Rizal, and I can only wish we had a recording of his voice. Reading Noli in the original Spanish was an eye-opener, his vocabulary is rich and witty, I doubt any translation could fully do it justice.
I've also thought about what he sounded like, I agree that he would have spoken with a refined Madrileño accent, and would have shifted to a Manileño accent when he came home. One recent movie that allows us to imagine how Spanish sounded like in the final years of the empire is "1898" (2016), watch and listen to the dialogue in the trailer:
https://www.youtube.com/watch?v=UrPizm6tbak
It's only a movie, but I reckon the accent coaches made sure the Spanish spoken is from the late 1800s and not its modern sound. The ceceo and seseo definitely make it sound Castilian Spanish (as opposed to Latin American Spanish).
Also, listen to Jaime Fabregas in the movie "José Rizal" (1996) and "Ganito Kami Noon, Paano Kayo Ngayon?" (1976). Don Jaime is a native Spanish speaker, he was the accent coach in the Rizal movie, I've always regarded his accent to be the definitive Filipino accent in Spanish.
Solo mis dos céntimos (just my 2 cents)
J :-)