I disagree that they are the same in the eyes of patch management. They're kept the same version just like Chrome keeps their embedded version up to date with Adobe's stand alone installer.
My remediation center reports win10 clients as needing MS18-03-AFP but those win10 machines are not applicable for APSB18-05.
Any win7 client that needs Flash working in IE is going to need APSB18-05. If you're not pushing out flash (lucky you!) other than built into win10, I'd think MS18-03-AFP should be good for you. Your applicability for each patch should give you an idea of what your scoped machines need.
I'll never understand why Microsoft chose to embed Flash (end of life 2020) into their operating system.