From what I can tell, the events are regenerated every time the guide is updated.It still has to track them somehow? Guide data gets updated every night (or however often it is), programming descriptions can change. I'd imagine the system keeps track of everything it does so that it can dynamically adjust to changes. Keeping the programs indexed is likely also essential to allowing users to go back and restore skipped programs that they happen to watch to re-watch. (Say a repeat of the last season finale before the start of the new season.) I don't think the problem is that the system keeps track of everything, it's that the event limit is not higher. Fix that maximum and the complaints go away.
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If your timer is for new episodes there is no need to keep those timers for last season's finale, since it's not a new episode.
As for the event limit, I agree that it should be increased. But, if there are valid reasons why it cannot, then eliminating the storage of skipped non-new episode events for only new timers would be another option...