Hi @JBranahl,
I found this old thread while doing a community cleanup.
This sounds more like a feature idea than a question, so you could always post in the ideas area if you'd like Instructure to somehow adjust Canvas. With that being said, as a Canvas admin myself, it seems like your school/institution may be doing things in a somewhat unusual way and that may be the root cause of the problem. In most cases, when using automated process to enroll students into courses/sections, there is no invitation generated for students to accept. Second, if you're using a single Canvas course shell for multiple different sections with vastly different (6 months) dates, I think there is always going to be come confusion. If most teachers at your school/institution agree, your team there may want to inverstigate using different course shells for each section. There are plussed and minuses of that approach, but one of the plusses is that you shouldn't have this rolling enrollment / large people list issue. Just a few thoughts off the top of my head.
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-Chris