The only difference I can tell between the two transfer speeds is that in the first, Transmit is telling you what's going on via the GUI. In the second, it's purely doing the work.
[robg adds: On my machine, I get only one "pop," when Transmit completes the entire transfer. I've tried various combinations of dragging from the Finder vs. using Transmit's window, as well as different settings in the Transfer tab of Preferences, but I cannot replicate this behavior. As such, files seem to transfer just as quickly whether I hide Transmit or not. I'm posting this mainly in the hopes that someone out there hears a file-by-file 'pop,' and can confirm (or refute) any speed differences.]

