"Efficiency" can only be defined in terms of something else -- you can be optimizing throughput or optimizing costs and you'll end up at very different solutions. One is efficient with respect to waiting times, the other is efficient with respect to costs.

In your latter example, it could very well be the case that steps Y and Z had purposes you didn't take into account that makes the new process less efficient in some cases with respect to the target metric.

Either way, overoptimization and focus on specific metrics to the exclusion of others is a real problem. Circumstances change over time and high levels of optimization make processes more brittle and likely to fail when circumstances change.