That case was one of a line of cases that go back to a New Deal decision that a farmer who grew wheat solely for his own use was nevertheless engaging in "interstate commerce" and subject to New Deal quotas. If that case were reversed the conflict between federal and state marijuana laws would no longer exist.
What I believe Thomas is saying without actually spelling it out is that as long as Federal legislators skirt their obligation to spell out the actual law on this, it’s a mess at all levels of law.
“What Thomas is saying is that Gonzalez v. Raich was wrongly decided”
No, that’s what he said at the time in his brilliant dissent; what he’s saying now is that the facts on which the Gonzalez majority’s argument was based no longer apply.