How to open new windows as separate application instances for Chrome, Terminal?
You can try the following syntax using open command:

open -na "Google Chrome"


where -n parameters opens a new instance even if one is already running.

Adding extra --user-data-dir will start instance in the separate profile directory, e.g.

open -na "Google Chrome" --args --user-data-dir="$PWD/Foo"


And using --profile-directory you can change the default profile name.