Bash subshell in Terminal has Mac OS's session save enabled
I’m not certain when this became the default, but I agree, it’s an annoying default; it was added in one of the last few major releases. I came across this question because I was searching for how to best disable this, and I think you may have provided the solution yourself:

In /etc/bashrc_Apple_Terminal, there is great amount of documentation about how the functionality in the file is implemented.

The final comment is the kicker:

# The save/restore mechanism is disabled if the following file exists:
#
#   ~/.bash_sessions_disable


I tested this on my machine and it works, no more session saving.