It's about practical and useful gearing. With a geared bicycle, you want the gearing to be a good match with your fitness and your riding terrain/conditions.
If you are a very strong rider with incredible power output, a very tall ("max") gear may be of some use when sprinting in a race or while descending a mountain pass. 52:11 is a huge gear, and 52:12 and 52:13 have very limited, practical use. When you factor in that the R3 and R4 only have 8 cogs (with the largest two being poor choices to use with a triple's outer ring), you might notice that you'll very seldom use that large chainring at all with an 11-28.
If you have some riding experience, you can use an online gear calculator to see just how useful a particular drivetrain should be for you.
The 50:12 available with the two upper models is tall enough to hit 30mph at a relatively modest cadence of 90. The 12-25 also has fairly close spacing with its nine cogs; at the higher ratios, the spacing is only one tooth, whereas the 8-sp 11-28 cassette makes you jump two teeth in the top ratios. This is more user friendly.
Road cranks used to commonly come with 42t inner or middle rings (double or triple cranks, respectively). More recently, that has been scaled back to a 39t on most triple cranks, reducing the ratios ~8%. I get more use from a 39t ring than a 42t ring, but ymmv. And, not that it's material information to your question, you're correct about the difference in component quality. Even in its lower product series, Shimano cranks and bottom brackets offer better shifting performance and durability than FSA products.