I think I understand your use-case, but I want to say it back to you in more detail so you can correct me and elaborate just a little more. Especially, because I will argue that this use-case is better served through extant features of gradle.
I think your use-case works like this:
1. You have an automated build (maybe a CI server) that is running your build and tests.
2. Occasionally, you find that a test has become flakey.
3. Now, you want to be able to exclude this test from the tests which are run as part of your automated builds (while notifying owners, etc, that this is flakey.)
You state clearly that you don't want to have to modify the codebase for the pipeline to be able to exclude the tests. However, I don't understand yet the motivation for this. Why not modify the codebase?
The main argument for going ahead and modifying your build files or the annotations on the flakey tests, or something in the codebase is that you keep all of the configuration of your automation in a single, portable place where the entire development team can keep track of what changed and why (in the commit records).
If you only exclude the flakey tests in the configuration of your build pipeline by modifying the arguments you pass to gradle, then your collaborators may end up checking out the code and running tests which are known by you to be flaky (because you excluded them in the pipeline configs,) and becoming frustrated when they investigate the failures only to find out that they were known to be flakey.
One of the design principles which leads us to be reluctant to add lots of command-line options to Gradle is that we want to avoid the situation where institutional knowledge is captured outside of the project's build configuration. We are aware each time we add a command-line option we are inviting our users to encode yet another variation on their build process in configuration files separate from the codebase.
All three of the previous paragraphs of this mail are intended just to explain why we think you should be very reluctant to desire this feature. If you've read them and remain convinced that you still need this feature, I'm happy to review your work as you progress toward the enhancement.