Some schools have more sophisticated enrollment priority. For example, a department can assign priority or reserved spaces in specific courses by class level, declared major (or undeclared), etc., so that those with low priority for the course can only get on the wait list until after all of the students with high priority for the course have had a chance to register. And the school may use a multi-phase registration system, where all students can register for up to about half of a full time course load before any student can register for the rest. Schemes like this can be used to ensure that declared majors get their majors’ junior/senior courses before non-majors fill them up, and undeclared frosh/soph students can find space in frosh/soph courses that they may need for majors of interest (yes, this can mean that frosh/soph students may have priority over junior/senior students for popular introductory level courses, since the junior/senior students do not need such courses for their majors).
If an honors program with enrollment priority existed at such a school, the enrollment priority would only give priority within a given group (by class level, declared major (or undeclared), within a given phase, etc.). Perhaps the students in the honors program could be given priority for honors courses that are associated with the honors program.
For athletes, the schedule constraints of athletic training means that they have more limited time slots to choose from.