Mathematica currently cannot Export comments to basic Excel’s formats. But you can export your data with comments to Excel’s “XML Table” format which AFAIK is completely equivalent to the basic Excel’s formats .xls and .xlsx.
The basic idea is that you can save an Excel Workbook in the “XML Table” format, then import the generated file in Mathematica by the command:
Then you can find yourself how the comments are represented in the XML. It should not be too difficult to write a function for converting Tooltips into comments in such XML file.