What you see is actually unusual. Epplus does not actually generate the full XLSX file, but creates raw XML content (all Office 2007 document formats are xml-based) and puts it in a zip file that is renamed to XLSX. Since it did not start through the Excel engine, it is not fully formatted to stand out.
If this is a simple data sheet, then most likely Excel does not have to calculate much - just basic formatting. Therefore, in this case, he will not offer you to save. But even then, if you do, you will see that he slightly modified the XLSX file. If you really want to see what it does behind the scenes, rename the file to .zip and look at the xml files inside before and after.
The problem you are working with is that it is not just a simple table export. Excel should run the calculations the first time it opens. It can be many things - formulas, autofilters, column / row outsourcing, presentation, etc. Basically, everything that makes a sheet a little “different” after excel has done it.
Unfortunately, there is no easy solution for this. Running it through the excel DOM would somehow be simple, which, of course, defeated the goal of using EPPlus. Another thing you could do is to see the difference between the xml files before and after (and there is a bunch that you have to look at) and imitate the fact that Excel will modify / add manual editing of the contents in the "after" version of the file XML This is not a good option, depending on how extensive the changes are. You can see how I did it in other situations:
Create Pivot Table Filters with EPPLUS
Adding a specific autofilter in a column
Set grid color with EPPlus?
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