What format does the final file use by default?
MP3 at 128kbps by default, even when every loaded track is WAV, the Audio Joiner does not detect the format from the first file's extension the way the Audio Trimmer does. You can switch to WAV or to MP3 192/320kbps before exporting, if you need more quality or a lossless file.
Does the crossfade I set apply equally at every transition?
Not necessarily. The real overlap at each join is the smaller value between the requested crossfade and the duration of each of the two neighbouring tracks. A 0.4s jingle between 30s and 40s blocks, with 3s of crossfade requested, ends up capped at 0.4s of overlap on both sides, because the whole jingle cannot hold a 3s overlap.
Does joining files at different sample rates lose quality?
The lower-rate track is resampled up, to the highest rate present among the loaded files, never the other way around, so no track loses bandwidth because of the join. Resampling uses a Blackman-windowed sinc filter, the same kind of band-limited filter that avoids the aliasing typical of a simple linear-interpolation conversion.