As far as I know, unless you can pull data at the user level where you can also pull in a unique ID for each user and use that to dedupe, there isn't a good solve for this. It is hard to pull data at this level of granularity using the API because of the row limitation.
My first question is, if you need this level of data could you build whatever report this is in Adobe workspace rather than in another tool?
Second, is it important to have these numbers be the same when you know what the discrepancy is. This is a case where either report is wrong, one just may be "more correct" depending on the business question you are trying to solve for.
Finally, are you using CJA or AA? If CJA, they are making a new connector that will eliminate the 50k row restriction.