What is cellranger doing in comparison to other methods?
cellranger mkfastq is not necessary anymore.  It used to be that the cellranger software wanted the reads to be interleaved, and you could use cellranger to do that for you if you couldn't do it yourself.  Newer versions of cellranger will take the fastq files just like Illumina's bcl2fastq makes them.

Cellranger count aligns the reads, filters away duplicates based on UMIs, tries to figure out which cell barcodes really captured cells, and tells you for each cell barcode how many reads hit each gene.  You can go through the .bams, and see which reads were counted for what gene and what barcode, based on the flags and other tags in the .bam

If you want another pipeline to compare to, you can use the McCarroll lab's DropSeq pipeline, which is a bunch of little scripts, around the output of STAR aligner (just like 10XGenomics uses).  I have put the same data sets through both 10X and Dropseq, and they return about the same thing.