I’m sorry, I’m still confused about the behaviour you’re describing (my misunderstanding I think).
Are you able to share any example calls and (subset) results?
I’m unable to reproduce this using, for example:
twurl "/1.1/statuses/user_timeline.json?screen_name=tweepsmap&exclude_replies=false"
This shows me replies sent through that account as well as organic Tweets. Additionally, using the same on my own logged-in account, also includes replies as expected.