According to our understanding, all IE failures are captured in AS ABAP stack while AE failures are captured on JAVA Stack in CBMA scenario. Can you let us know if this is appropriate understanding
---> This is correct.
We have a requirement to customize these alert messages and will appreciate if you can tell us the way to do it?
You should look for the report SXMSALERT_SEND_VIA_MAIL as it is the one which we use to fetch the alerts when we setup CBMA.
AFAIK -This would be the only source to customize your alerts.