The parenthetical is evaluated separately from the sentence. It would equally read this way:

He's definitely a weirdo at times but he's a good guy, (I mean that in a positive way, for instance he likes old movies and watches them constantly, but when he says a movie is good he has never been wrong)

as the way I originally wrote it:

He's definitely a weirdo at times, (I mean that in a positive way, for instance he likes old movies and watches them constantly, but when he says a movie is good he has never been wrong) but he's a good guy

The "but he's a good guy" never syntactically follows the information about the movies, it is always tied to my opinion that calling my friend a "movie fanatic" isn't a strong enough descriptor and he teeters on the verge of being weird about it.

Nah. The "but" differentiates a positive trait from a neutral trait, and the parenthetical phrase clarifies that the neutral trait isn't necessarily bad.

Yes. The fact that you have to qualify that the ‘neutral’ trait isn’t ‘necessarily’ bad implies that you think people might think it was bad.

You wouldn’t need to qualify it otherwise.

People might think anything is bad.

Yes, which is why we only qualify it when we are implying it is a possibility.

Your comment doesn’t make you look stupid or casually dismissive.