I would be interested in understanding what you think Bazel's strange decisions are. Prior to Bazel, I had also used some of my own custom build systems--I was multiple rewrites into it--and I had independently come to some of the same conclusions as Bazel, such as the need for target syntax that separates the package name from the target name within the package (like how Bazel specifies targets as //dir/abc:def).

There are a number of other Bazel decisions that seemed strange until I tried to figure out how I would implement some particular feature.

My conclusion is that there are lots of small reasons why build systems are a pain in practice, and that the problem is a lot more complex than most people give it credit for.