The best reason is probably that the person creating the system doesn’t know at the outset exactly how, or even if, what they are building will work.

Excel often gets used for prototyping new models. A new model for allocating overheads - try it in Excel and see what the effects will be. A new forecasting method - get a ballpark estimate of the impact on the bottom line in Excel.

Once the model is in Excel it isn’t cheap or easy to get it out, so it often just stays that way, accumulating technical debt.