It also just kind of makes Alucard's whole thing (being the descendant of Dracula who rose up against him) kind of irrelevant if the entire Belmont clan is also Dracula's descendants.
I don't think that's really true.
CV3 says that the Belmonts were feared and hated, and that they were unjustly driven out of town for the "evil" supernatural ability which they had used to defend the people from evil. The recent cartoon says that it happened when Trevor was just an innocent little kid.
CV Legends says that Sonia was Trevor's mom. She was born with abnormal supernatural ability, and her grandfather recognized it, so he gave her the family's magic whip and taught her how to use it to fight evil. And in 1450, she did. She also bumped into a young Alucard, the half-Vampire who was not evil, but who was not yet actively fighting Dracula, and they had a one night stand. After her adventure, Sonia realized she was pregnant, but nobody told Alucard that he was the father.
I don't think this particularly conflicts with the 11th century stuff with Leon and the origins of the Vampire Killer whip. And it doesn't mess with the 100 year thing if Dracula somehow escaped his encounter with Sonia and it took him 25 years to recover and rebuild. And it supports the idea of the people turning on the Belmonts if Sonia gave birth to a monster-baby out of wedlock.
26 years later, in 1476, Trevor (who is 1/2 a supernaturally-powerful Belmont, and 1/4 Vampire descendant of Dracula, but shows no obvious signs of being a Vampire), meets up with Alucard and Sypha and they take down Dracula in one shot. Trevor and Alucard are clueless as to their relation, and the subject is never discussed. Trevor goes on to marry Sypha and mixes the Belmont bloodline (which has traces of Vampire in it) with the Belnades bloodline, so now the Belmonts carry wizard magic potential as well.
100 years later, in 1576, Christopher Belmont fights Dracula, but he's unable to finish the job so he has to fight him again fifteen years later in 1591.
Leading to Simon Belmont's CV1 adventures in 1691 and 1698. Which leaves weasel room in the 100 year rule for Shaft to bring Dracula back twice, in 1792 and 1797, for Rondo and SotN. And at the end of SotN, Richter Belmont's sister-in-law Maria Renard runs off to cheer up the depressed Alucard, but they probably don't have sex, as the immortal Alucard has decided to deliberately end his own bloodline through chastity (not knowing it already lives on in some small way with his allies, the Belmonts, due to that fling he had with one of them).