We can argue two ways here, to the same general outcome...
We can say with good conscience that the two classes were very dissimilar. Perhaps the configuration with the nacelles dangling on long pylons is advantageous for high speed, but tends to wear down somewhat faster? Also, high speed is an asset useful to all starships, but very
high speed might be something of a silver bullet. Perhaps Starfleet wouldn't need all that many record-breakers, as compared with slower ships otherwise carrying the same gear.
Indeed, we can argue that the two classes weren't all that different, save for the warp engine configuration, the impulse engine type and so forth. Sooner or later, it would turn out that standardizing on a single design would serve all the purposes previously sought with a variety of designs, and some random factor might have Starfleet favor the nacelles-down variant.
Military history is full of examples of this happening, really - when you look at WWII tanks, say. The Sherman chassis was picked out of multiple basically equal options and put to a variety of uses, with varying turrets, and eventually a few of those variants gained longevity (some may still
be serving!) while others disappeared completely, being retired or modified into the more useful types. On the other hand, towards the end of their service lives, these veterans again received diversifying refits: their ownership was now diverse, and no single user would be mass-producing any particular variant.