Without diminishing the other comments, it crossed my mind that the issue here is probably not whether Excel was used in the research. It's one of getting backup (supplementary) data into publishable form. That'd occur after the authors(s) had written their paper using their normal toolset for their work and gotten the paper through review. At this point, they are supposed to package up their data in some format dictated by the journal they are publishing in. Apparently .xls is an acceptable format -- which is not irrational. The format is documented and widely supported.
Anyway, the authors are just cleaning up and getting on with their lives -- cleaning the glassware (if any), paying any bills, archiving their data and scripts, returning borrowed equipment, etc. They are going to convert their data to .xls using whatever quick and dirty tool they can find. I doubt they are going to type tens of thousands of genome codes in manually. They'll use some tool they got from a buddy or write something themselves in Perl or Python or whatever scripting language they know. And they'll check the output to make sure that Excel loads it and that it's about the right length and that the first page or so and the last page look reasonable. And off it goes.
I don't think most folks outside of IT (and probably most in IT) are all that aware of Excel's flaky and sometimes bizarre data conversions. And, assuming that there's an unambiguous one to one translation between gene codes and excel mangled gene codes, this probably isn't a big deal. Anyone using the archived data will scratch their heads, maybe ask around, figure out what's happened, fix the data, and get on with THEIR research.