Compare multiple alignment results' aligned bases
I don't know of a single tool that can read multiple sets of BAM files and compare them. But you can use the Sam_Reader python3 module to create a csv file that summarizes each position in the genome for each of your 3 results and then compare them manually.

It should be installable with:

pip3 install sam_reader


And then generate the CSV with 

from sam_reader import Sam_Reader
my_files = Sam_Reader('my_bam_file_or_folder/')
my_files.per_base_stats(write_file='new_file.csv')


*but FYI this module requires pysam, which does not work on windows