I have been in software industry for 15 years and this happens all the time, being forced to release unfinished features, asked to ignore security, backups, etc. I would imagine same thing happens in other industries.
From my non-aviation perspective, it looks like they basically pieced together a bunch of complex systems, with each team making a number of (different) assumptions about each system. The systems themselves were influenced by FAA requirements to maintain the old certificate, which meant that certain desirable changes were impossible, so workarounds were devised. The problems were due to misunderstandings about how the systems would work when assembled, and these issues were not discovered and/or communicated. It really seems like a systems engineering problem, aggravated by a number of external influences (including business reasons and certification).
It is supposedly costly in time and money to acquire a new rating but it has been done obviously.
The airlines wanted a single pool of interchangeable pilots flying in name interchangeable planes (their existing 737s and the 737 MAX). Supposedly one of the airlines threatened to take new business to Airbus and had penalties written into the contract to make the 737 MAX fly under the existing certificate.
So it wasn’t the old certificate driving these issues, it was Boeing and it’s customers wanting to maintain the old certificate that drove the issues. That is a very large difference.
The FAA may be in the right or in the wrong, but it has made certifying new designs almost prohibitively expensive and time-consuming; for evidence of this, simply look at the Cessna 172 (still in production on a 60-year old certificate), and what happened when Bombardier tried to put a new airliner into production.
You're definitely right that the airlines wanted interchangeable type ratings for crew, but the issue slightly more complicated than you're painting it.
I never argued the old certificate forced the issues, the certification system just strongly incentivized 'upgrading' the 737. This was one of many causes.