Not sure if this is intended behavior or not: when restricting alignments to regions via -t, the number of filtered reads does not reflect the region subset https://github.com/samtools/samtools/blob/develop/stats.c#L1157. With -t one would expect to see only stats from reads overlapping the regions. One can work around this by streaming through samtools view -L but, unexpectedly, view -L and stats -t can give different number of raw alignments.