If I select a GDB, and select export multiple, to run the tool, when the tool opens up, I am seeing all my data in that GDB already in that tool. I don't want arcmap to prepopulate. Is this expected?
Yes, this is expected because you are launching the Feature Class to Geodatabase (multiple) from the context menu for the Geodatabase. If you want to launch the tool without any paramaters populated you can do this by accesing the tool from ArcToolbox or the Search Results.