I believe either of those approaches should work.
From what I understand, internally ArduSub uses quaternions instead of Euler angles, so the firmware itself can’t experience gimbal lock. The issues come about when commanding Euler angles in or reading them out, because the conversion reintroduces the gimbal lock issues. To handle that you can effectively lie to the autopilot about the orientation it’s in, so that you shift the gimbal lock to orientations you don’t expect to operate in, which takes it away from those you do (horizontal and vertical).
I just tried setting Roll90Pitch315 and the vehicle by default shows an orientation of 45, and straight down shows negative 45. Going straight upwards goes through gimbal lock at 45 degrees on the way to pointing upwards, so if you want to be operating vertically upwards then you either need to rotate the Pixhawk instead, or need to add a custom orientation of Roll90Pitch45 to your ArduSub build. Hope that’s helpful 