The LFForm.setFieldValues function returns a promise so the actual action is not guaranteed  to happen before form submission. The onFormSubmission function only supports synchronous callbacks right now which explains the behavior you are seeing. You could try the following code, but I doubt you would experience what you are requesting. That being said, this is a valid use case so I've created #521888 to handle asynchronous callbacks in the event functions in the LFForm object.
The onFormSubmission function should accept the async callback, please try the code below and let me know if it works for you.

LFForm.onFormSubmission(async function () {
    var fieldsToClear = LFForm.findFieldsByClassName("clearThisField");
    await LFForm.setFieldValues(fieldsToClear, "");
});

EDIT: I actually confirmed with the team, this handler should accept the async callback so this code should work for you! I will make sure the documentation gets updated to reflect that