It does help in that the secrets are not in plain-text, readable for any script you run. With 1Password, a process asks for the password and it gets transferred not through the filesystem but through IPC. 1Password shows a dialog: "Do you want iTerm to get your SSH key ABC123?"
In my thinking, this is more secure than plaintext in filesystem
If your system is compromised, it doesn't matter what you are using: the attacker will get the password for whatever secure thing you store your secrets in.
Sure, but is your system compromised because someone left a key in plaintext? Attack surface is finite and can be meaningfully reduced.