It is only the final report(s) for the end-users that have this limit (that's what the Designer is for), and that should be fine. It should not be necessary to create a report with more than a few thousand rows to look at. When the users want to look at / search the detail data, I create a list report with a control object at the top (a drop down filter etc, or a text search box) with a default value that returns less than 40 000 rows. You can add multiple filters so the users are always able to return less rows than the limit (and add a text box with a warning about the limit). This works fine, your list report will always show a default filtered table, and the users can search or drill down to retrieve the rows they need.
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