No, it
really is a problem with this design and not an issue with golangci-lint.
The trouble is that MVS will happen across all of your dependencies, including direct and other tool dependencies. If everything very strictly followed Go's own versioning guidelines, then this would be OK since any breaking change would be forced off into a separate module identity. However, even Google's own modules don't always follow this rule, so in reality it's just kind of unrealistic.
You don't need something huge like golangci-lint to run into problems. It's just easier to see it happen because the large number of dependencies makes it a lot more likely.