Question: How can the percentage of reads aligned to "Exonic Regions" be greater than those aligned to the "Transcriptome"?
Answer: "Reads Mapped Confidently to Transcriptome" is a subset of "Reads Mapped Confidently to Exonic Regions." A read that is compatible with the exons of an annotated transcript, and aligned to the same strand, is considered mapped to the transcriptome. If the read is compatible with a single gene annotation, it is considered uniquely (confidently) mapped to the transcriptome.
For more information please see the Cell Ranger Algorithms Overview page on our support site.