If you are setting the testing environment variables to your requirements then many of these problems should be eliminated. If a test suite doesn't honour the variables then that's worth raising as an issue against the dist in question.
Don't run extensive "timeout" tests unless you absolutely have to.
If you are referring to idle timeouts then installing/updating your modules in parallel can mitigate that. However, I agree with you and long timeouts should not be part of a standard test suite at all.