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For some workflows I see the value of concentrate a high number of formulas in a single Formula Tool, specially when you have a considerable number of simple and independent formulas. This makes future changes to the workflow easier, since you (and other in your team) know where exactly to find the formulas in a workflow. But as higher the number of formulas in Formula Tool, more difficult is to find a specific formula in the tool.
My suggestion is to implement a sort option - so you list the formulas/columns alphabetically - and/or a filter option - bringing the relevant formulas/columns as you type.
Since I am relatively new in the Alteryx world,I am not sure if there is an alternative for that (officially or unofficially speaking).