These custom audio settings are accessible from the Audio mode tab when the Audio scan mode is set to Custom.
Amount of file to compare in seconds
This controls the length of the audio (from the beginning) to be compared. So, if it is set to 120 secs then ONLY the first two minutes are compared - anything later is ignored. Clicking the 'Match full length' option will match the entire length of the audio. Note that the longer this length is the slower the process (and larger the audio database).
The matching threshold setting. The threshold setting may be set up to 100. This isn't a percentage similarity - tracks matching on a 100 threshold may still have differences.