Is there a specific demand to compare using Excel?
If so, consider that there might be rounding issues regarding to the number format that gets exported to Excel, which, as i understand, also depends on universe settings (in case of that) or number conversions in Webi itself. So first thing to do is to check if the excel export itself contains the same values than you would expect in webi.
As you are in 4.2, you have more limitations than you would have in 4.3, like you cannot use OData to access the old BI platform or use Webi as a data source. So i see why you are trying to use excel. But when it comes to differences on that decimal level, it more looks like a data/number conversion issue when exporting the report as excel between the different SP releases, so i would then not export to excel, but to a plain text/csv so that there is no other application doing something with number formatting or conversions like excel could possibly do. Then, comparing text files can be done easily with lots of tools that offer some sort of automation and are free - like Notepad++ comparison or command line tools like "fc" in windows - linux even better tools available i guess -, also using regex to sort out those minimal differences.
of course it depends on the number of reports you need to compare how much time it makes sense to spend in an automation comparison on that level.
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