IME, the fees are technically for a re-issue. I haven't done a change like this in a long, long time, but I believe if you make multiple changes at once (i.e. say you make a date change both the outbound and return at the same time), you are only charged the fee once, since it would only be re-issued once. Likewise, when you cancel a non-refundable ticket, the itinerary is canceled and you aren't charged a fee at that time - but is changed when the ticket is re-issued when you specify new flights.

Almost all changes require a re-issue. There are certain smaller changes that don't - changing the date of a ticket on the same routing is still changing the flights, so should require a re-issue. When you get CPU'd, however, this is an example of a change that doesn't require a re-issue.

In your fare rules, I don't see where a fee would be required for a schedule change. In fact, clearly states, 'waived for schedule change'. I know there used to officially be a '2 hour rule' where changes 2 hours or more (or a connection falling below MCT) allowed one to change without fee. And while technically, anything else required one to pay the fee, in reality, most agents were somewhat flexible - you're not going to get a free change with, say, a 5 minute schedule change, but probably an hour, with some agents, perhaps less.

Are you worried about being charged a fee for something other than a few minute change? I wouldn't be.