On an expendable architecture the priority is saving weight on the second stage, because every kilogram saved there saves many kilograms for the first stage. So pound for pound the second stage usually costs more than the first stage. Also the cheapest way to build a first stage is with one or just a few big engines. Both these optimization criteria are reversed for a re-usable design. In the Falcon 9 the first stage is re-used while the second stage isn’t, so that’s the stage you want to spend your money on. Also a few big engines can’t be throttled low enough or gimbaled precisely enough for a landing burn. Even the using just one of the relatively small engines in the Falcon 9 can’t be throttled low enough to hover. Hence the Falcon 9 has many smaller engines to give it a much greater range of thrust settings and better attitude control.
In fact optimizing the Falcon 9 for first stage re-use has lead it down a very different development path from most modern launchers.
Since they took four months to refurbish this stage it may have cost quite a bit to do so for now. But they're learning and Block 5 to debut later this year will have lots of changes based on what they learned.