Your complaint is the designer’s lament, regrets because fast iterations will usually beat a cohesive development, the struggle to accept that the imperfect delivered today wins versus the perfect delivered tomorrow. A good engineer chooses their battles, fights for the right compromises, and grudgingly accepts that the evolutionary remnants in all our engineering artefacts are the price we pay for the results of iterative path dependency. For example, Intel didn’t design the x64 ISA.

  Practice beats perfection
  The engineer’s game we play
  Make do with what we've got
  And make it work today

If you watch Jim Keller talk about microprocessor design, he seems to say that designs converge due to real world constraints and factors. Human designers are imperfect, which Jim seems to be very good at acknowledging. Every now and then we get to refactor, and remove some limiting kludge. But the number of kludges increases with complexity, and kludges are the result of compromises forced by externalities, so the nirvana of a kludge-free world can only be reached in engineer’s fairy tales. Disclaimer: I was an engineer type, but turned dark by the desire for the fruits of capitalism. (Edited)