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These are some of the nuances of using Output vs Render that you'll need to decide what works best for your case. When using the Output tool, you are able to specify the output range and keep cell formatting, but numeric fields will be output according to the Alteryx numeric format. In Alteryx, if you want comma separators, those commas are considered string characters (depending on localization settings) and that requires a string field.You can convert numeric values to strings and add the commas with the ToString( function which has an optional third argument for those commas.
Things works a little different for the Render tool. You cannot specify a cell range, but the Table tool can create a Layout that includes numeric values with comma separators in Excel.
Also, what version of Alteryx Designer are you using? I haven't really tried out the new Excel enhancements that are a part of v2020.1.