Good call out! Thanks for posting this warning.
As far as I know, the schedule should be fine, since it's processed server side, which means it should finish processing the data, then build the file, then send it....
I've not used this process much though... normally I use the Data Warehouse or Report Builder to pull out data.... but I do know that both of those cannot get the data in the same format as the Workspace...
I think it's a good rule of thumb to make sure that the data is fully loaded prior to exporting, and as always, confirm that the resulting file is as expected!