Because he genuinely has a somewhat idiosyncratic style of legal reasoning even though ideologically he's a run-of-the-mill conservative hack.
He's not run-of-the-mill. He's the only justice who has called for Batson v. Kentucky and NY Times v. Sullivan to be overruled. He's the only justice who has ever compared Planned Parenthood to the Nazis. He's the only justice who has ever cited James O'Keefe.
I know what you mean, and Thomas is one of my least favorite people in American public life, but in fairness to him, presumably the two justices who dissented in Batson (the incumbent and immediate future Chief Justice, no less) also felt that it ought to be (if possible) overruled.
Did Chief Justice Burger and future Chief Justice Rehnquist (the dissenters) want Batson overruled? Rehnquist had the chance to overrule Miranda v. Arizona and refused. We know Kavanaugh doesn't want to overrule Batson.
Well, there is substantial history of justices dissenting from a case when initially decided but declining to overrule the precedent in a later case. That's a big part of how the Supreme Court works institutionally.
Consider: Roberts dissented in Obergefell back in 2015. Could you ever see him joining an opinion overruling it now?