I think many people fall into the same trap with AG combos. They see a large 2 HP pump with a moderately sized filter and assume it is over-sized when in reality it isn't that bad for the reasons that mentioned. You just need to be aware of what you are getting. For a typical AG pool, the combo I mentioned would deliver a little over 50 GPM and if you go by the APSP-15 residential specifications, that would require at least a 145 sq-ft filter so a 200 sq-ft filter is fine for that pump.
Both Hayward and Pentair seem to size their combos appropriately just based upon the spec but they are at the upper limit of pump size and lower limit of filter size so it doesn't hurt to go larger with the filter or smaller with the pump if possible. It's just that with the combos, you don't have a lot of choice. However, even if you want a smaller pump, you could always just downsize the impeller which doesn't cost much to do. You would just need to price it out both ways.