This should already return only filtered projects because it uses vitest.projects and not vitest.resolvedProjects. Why doesn't it?

Yes, but in those cases where we have different projects defined by defineProject, the filter of files.flatMap(file => this.getModuleSpecifications(file)) is returning TestProjects beyond what it should.
Because of this, one of the possible solutions would be to apply the filter by name.

You just rephrased what I asked. Why does it do that? getModuleSpecification shouldn't include filtered out projects

Sorry, now I understand your question...
getModuleSpecification has the following validation:

const _cached = this.getCachedSpecifications(moduleId)
if (_cached) {
  return _cached
}

When we are re-running the tests with the filters along with --watch it ends up returning the cache projects instead of trying to search again. (Another solution would be to simply remove this validation and cache return).

@sheremet-va Do you have any idea what paths we can take to solve the problem? Insert validation into specificationsWithFilterByProject or remove cache validation for getModuleSpecification ?