I think the binary prefixes only add confusion because almost everyone uses powers of 10 to count things.

I do not think it is true.
Anyway, so you do you want to use prefixes for both places or use exact number for both?

The lower pane displays KiB, MiB etc. The upper pane does not use any prefixes to display file sizes. I think the binary prefixes only add confusion because almost everyone uses powers of 10 to count things. I would prefer that WinSCP use SI prefixes, e.g. 1234 MB for 1 234 123 123 bytes, not 1205 MiB.

I'm lost, please try again :)

The queue pane displays the transferred amount of bytes with binary prefixes (MiB) but the explorer-style file browser pane uses plain integers without any prefixes. SI prefixes would be easier to compare.