Encoders or not, one or 2 IMUs, what FW would be useful information to provide and also what exactly are you trying to configure.
The gimbal can be just simply rotated upside down, are you trying to start upside-down? is camera upside down or only gimbal. how have you tried to configure it?
just part of the gimbal is rotated upside down so i have the yaw in the bottobm, all the rest is in the standard position, the tiny board has the orientation of standard gimbals, the IMUs are oriented in the standard direction, Z up -X right
no flipped elements except for the YAW motor and YAW arm
this gimbal will only work in this configuration
pay attention to the fact that also if i have encoders i can't activate them until i don't find the good tuning
basically i have the ROLL axis that doesn't stabilize
it looks ok untill you don't move the gimbal then it starts to woble slowly, the impression is that as it comes close to the stop point it bouces back and tries again to arrive to the stop point looping this way forever
i changed the ROLL motor twice, i changed the main board, i removed the unnecessay elements in the gimbal to find the perfect balance but nothing worked, the ROLL keeps wobling
If you always use like that and have not even tuned it yet, for get the hole upside down setting, just set the gimbal to work on that position as normal position. I.e. do the basic setup on that position.