If I run GUI applications, let's say, as my user -- as is the default in most operating systems -- they have general access to my files, including my keys-as-files, no? (Putting aside some minor restrictions MacOS and others are slowly making.)
We implemented support for password-encrypted keys for the cases where you store the key file in, say, Dropbox.
There really isn't a point to defending against code running unsandboxed on a single-user machine.
Most people don’t add a password to the disk encryption, meaning the keys can “easily” be extracted by MITM the contacts on the chip.