...WAV and FLAC list similar transcoding statements as ALAC does,
No, that is a very different statement. It applies only to the original SliMP3 and the first generation Squeezebox 1. No one is talking about those models in this conversation.
Here's the WAV/FLAC statement: "- Must be transcoded (automatically) to play on SlimServer with older (SB1/SLIMP3) hardware"
Decoding for WAV/FLAC in all later Squeezeboxes (version 2 & 3/Classic; Duet and Transporter) takes place natively in the unit.
As to file streaming settings, there is a settings link at the bottom right of the Squeezecenter web page. Locate the "file types" settings for the server. The "convert.conf" file can also be directly edited.
There are a number of important settings in Squeezecenter that impact sound quality. As true open-source software, they give you as much rope as you need to fine tune things or really screw them up. ;-)