That kind of mismatch and contingent arbitrariness bothers me too. But maybe it's like learning a language, or inventing a language, or developing a legal system of laws and precedents, or developing an industrial economy's repertoire of standardized part types and specifications, or evolving a biological system of hormones and signaling molecules. Not something you can do perfectly in advance (insofar as that could even mean anything), and yet not something you can simply do without either.

One in-between option is to develop an eye toward something like what software engineers call "technical debt": temporary commitments that will need to be reworked later if that whole part of the system is not to eventually become unsustainable and have to be thrown away entirely.