I completely see your point, and my boring response is "it depends". How heavily I rely on my personal organizational setup depends a lot on context. For instance, at $WORK I need time-tracking and tracability of tasks due to audits. Having a system I barely have to think about is crucial to me in this setting not to waste time in horribly slow web-based ERP-systems. For personal projects I stick to a single text file of issues and ideas. Knowing what to use when is part of the general assessment imo.
For me, the crucial part is to create a tool/script that just gets one task done as fast as possible. I don't need tools that can do everything. Often it's just a bash script that executes like 5 commands to execute/build something, so that I don't even have to think about those steps and don't forget one.
Tho it is a really fine line to not get hung up on those organizational tasks, yes.
