When the writers were first creating Beast Wars, they honestly did not know a lot about Generation 1. They DID, however, originally plan for the planet that the Maximals and Predicons landed on to be prehistoric Earth.
When they started doing research... and found that the Autobots and Decepticons had also landed on prehistoric Earth, THEN they started writing in connections. And those connections were not just "tacked on" to the end of Season 2. They were connections that were a long time coming. The writers left clues in abundance.
In Beast Wars, Starscream shows up, Ravage shows up, and even Prime himself wakes up for a little bit. Unicron's head makes an appearance. There's talk of the Great War, and the Transformers connections with the humans. We see, via flashback, the crew of the Ark crashing.
None of these are "re-imagined" versions like Armada, RID, or such. We're suppose to be seeing THE Generation 1 Starscream, Prime, and such. Ravage is different, but he's given a backstory as to why he's different. They are on THE Generation 1 Ark.
Beast Wars Megatron even shoots Generation 1 Optimus Prime in the head in order to change the future.
I don't know how it could be any more clear that Beast Wars is a sequel.
There were even plans (though the writers disagreed on using it, and so it wasn't implemented) that the Vok were going to be revealed to be the Swarm from the Generation 2 comic books.
Chronologically speaking, it also comes after Generation 1, as Generation 1 BEGAN millions of years ago. Yes, they crash in the first episode, but by the time the Beasties have crashed, the Ark has already been there for some time. So, no worries about it being a prequel either
