While WER with respect to the full reference transcript (containing both fluent and disfluent words) is not meaningful for integrated systems intended to produce fluent output, WER with respect to the fluent subsequence is a meaningful measure of overall system, since this is the intended output of an integrated system.
since disfluencies only comprise around 6% of the total words, the WER score largely reflects how well fluent words are recognized, rather than how well the system handles disfluencies.