Failsafe behavior

It knows you haven’t taken off. If you’re still on the ground, the failsafe action is to disarm. This is normal, and was the expected behavior even before the changes. You can read about the changes here: Failsafe updates for radio, GCS, and battery... plus new FS_OPTIONS parameter

Setting FAILSAFE_OPTIONS to a value of 19 will ignore the GCS failsafe if you’re in a pilot controlled mode, and will ignore the radio and GCS failsafes when in Auto Mode. If that is what you want, good. But that is not what you described in your post. You said you want it to RTL when you’re in pilot controlled modes (such as stabilize or loiter), but continue in auto modes. In that case, you would want FS_OPTIONS set for 3.