I think you raise a good point that often gets forgotten. When you switch from a general purpose tool to something specific, you lose visibility and introspection tools.

I see people move from a filesystem based workflow to a database and while that may be faster and more efficient you lose those tools to look at and tweak data. You either need to write those or teach them how to navigate the database. People rightfully hate black-boxes as soon as stuff stops working as expected.

Personally, I love the Linux command line and will pipe stuff in and out or stash things in flat files. I may move the data back into a spreadsheet to get more visibility or look for trends.