Comment 2 for bug 87941

The readme.debian explicitly states the following, which just confirms your statement:

Only devices that are *not* listed in /etc/network/interfaces or which have
been configured "auto" and "dhcp" (with no other options) are managed by NM.

This way you can setup a custom (static) configuration for a device and NM
will not try to override this setting.

This is a duplicate of bug 5364 though.