Every few years AMCAS tries to upgrade their system and it never seems to go well. Some years back they unrolled a new version and the whole thing melted down. Schools had to resort to paper applications in real time. That was fun!
Things have evolved so that schools generally buy their own admissions management systems to deliver secondaries, collect fees, schedule interviews, collect feedback, etc.
AMP is a common one. These in turn have to connect to whatever underlying system(s) exist in the school (i.e. Banner, PeopleSoft, etc.). A portion of your secondary fees actually get skimmed by whatever software the school uses for this purpose.* AMCAS has been working on its own "secondary" admissions system for awhile, one which will presumably merge seamlessly with the main program, but it has yet to roll out.
So yeah, it would be great if AMCAS could do everything we want (well) and talk to every other system out there, but unfortunately it's not the world we live in right now.
*Ain't nothing in this world for free.