Why total RNA-seq usually yields low mapping rate?
A likely explanation is that total RNA-Seq contains a high fraction of reads from ribosomal RNAs. Ribosomal RNAs are present in multiple copies across the genome, hence many reads map to multiple genomic locations and get discarded by the aligner. For example, STAR with default parameters considers a read as unmapped if it maps to more than 10 genomic loci (this behavior can be changed with the --outFilterMultimapNmax option).
To confirm if this is actually the case, you could check the number of multi-mapping reads in the aligner's log files.