We're exactly on the same page: "the tool is not the goal". The only difference may be that I see chosing options for an app as options for a tool. If I want to cut wood or metal I need a different saw. Even though the tool is basically the same it doesn't serve the same purpose. Hence I configure options once and for all, like I would consider which hardware I need exactly in terms of use, ergonomic, power... before buying it.
I don't spend time tweaking the look of a tool because it's doesn't fit my approach of things anymore. As such I don't even use a DE. But I feel the need to build the right tool (i.e. system app) I need to perform a job as efficiently as possible while keeping the tool itself minimalist and as invisible as possible. On my daily use I have tools that I couldn't live without anymore but if you ask me a list I will either forgot them or put them at the bottom because I will not think about them right away since they became a second nature.
I certainly see the comfort of the out of the box approach and it can serve a lot of people. In my use case I just realize that - using the example above - it could be like using a wood saw on metal in some cases. It may work but not as good as you would expect to have the job done properly. Also, the fit them all approach means building an app with tons of options activated and I prefer to have available to me only the options I really need. The philosophy feels less bloated to me and I'm not overloading my system with stuff I'll never use. It's more time consuming at first to chose the right app but with time it became quick enough and it definitely save me way more time in the long run when I use my system.