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The logic that controls the order of operations has a number of influencing variables. Of course, the tool connections will influence order, but what if there are 5 input tools? In that case, the ToolID # typically controls the order of input.
You can check to see if this is the case by checking the Tool ID of each tool (Configuration window > Annotation) or in the results window: there will be a number in parenthesis for each line (like "Input (5)" ). See if these input tools follow an ascending numeric order.
Tool ID numbers are assigned when a tool is added to the canvas. So if you want to force something to the end, cut and paste it. The pasted tool will be treated as a new tool and get the next tool ID available. If you want a tool to be first, cut and paste everything else. You can also use Block Until Done tools (in the Developer category).
The point is that the tool ID doesn't matter because the Alteryx engine will make sure the workflow is processed in the correct order in accordance with the tool connections. If it's defaulting to tool ID values, then it doesn't matter which one is processed first.