JackIsJack
I think you are right to draw attention to the risks inherent in complex calculations hidden behind a name, but I wouldn't agree that makes it a bad idea. At the extreme, one has the chef's masterpiece, excessive presentation and style and almost impossible to deconstruct. At the other, there is the typical spreadsheet creation, more like something the cat has regurgitated; all the pieces are visible but I certainly wouldn't care to sort through them.
Putting culinary metaphors aside for the moment, I agree that Name Manager offers a poor user experience (though not quite as bad as conditional formatting and validation). On the other hand, there is nothing to say that you shouldn't use the grid for development and testing. Now as the nightmare of relative referencing is largely behind us, you can use any scratch space within the workbook for testing array formulas without affecting the result.
One of the plusses of Names is that they can capture the intent of the operation in business terms, so can provide a level of documentation in their own right. There is also the comment box that provides a possibility for further explanation. On the subject of helper ranges, they can be useful for checking detail but they add sheet clutter and make it difficult to determine the overall direction of travel. Very often it is simpler to check the output than it is to check steps of the calculation.