bashrc files are not run at startup, they're run at the start of every interactive bash shell session. If you never log in, they'll never get run. If you log in and out repeatedly (or, more realistically,
ssh in 20 times), they'll get run over and over.
Second, in general, everything in
/etc/ is system-wide, while everything in your home directory is just for you. So,
/etc/bashrc is run for any account's interactive bash shells, while
~/.bashrc is run only for yours. (Of course on a single-user machine, none of the other accounts are actual people who will ever run an interactive bash shell, so the distinction may not seem that important.)
Anyway, if you really want to run at startup, the right way is generally to create an init script (although in some cases you may be able to get away with using
rc.local or other mechanisms). See this doc for a basic primer on init scripts, and some Debian specifics.