X3 Pin3 breaker orientation

The X3 Connector functions as the interface for the (aircraft-) wiring harness. Refer also to the 912iS installation manual Chapter 76–00–00's section on Fitting the Amp connector. In Figure 3.7: X3 Connector: (Airframe) Wiring Harness side:

• PIN 1 is assigned to the backup battery switch.
• PIN 2 is linked to the start power switch.
• PIN 3 is utilized for the start power switch and bus.

Terminal 1 allows the option of supplying the EMS with external power in scenarios such as internal power supply failure. Terminal 2 facilitates powering the EMS during engine start-up to the point where the engine speed reaches the level where the internal generator can take over. Terminal 3 serves the purpose of providing the Airframe with electrical energy after generator A has assumed control of powering the EMS.

The output voltage for Terminal 3 is as follows:

• Minimum: 13.9 V
• Maximum: 14.5 V
• Nominal: 12 V

Yep, but breakers have a Line terminal and a Load terminal. Before start, Pin2 is a load. After start, the battery and avionics are loads. So the breaker can technically be wired either direction and be considered "correct" depending on whether the engine is running.

So, should the master switch be on the Load side of the breaker?

When deciding where to locate a breaker, you have to consider where the source of dangerously high current is located.  The charging system's output is inherently limited by the physics of the stator's design (permanent magnet flux, wire cross-section, rotational speed, etc.).  It probably wouldn't do the stator or regulator any good to short X3/3 to ground, but it also wouldn't result in a massive current flow that melts wires.  The bus connection, on the other hand, is directly tied to the battery via the master switch (the Rotax diagram is representational, not a schematic; in reality, the switching element is the battery contactor).  If the bus-to-X3/3 wire shorts to ground, the battery can supply wire-melting current.  The circuit breaker should be located as near as possible to the at-risk end of the wire: at the bus.  In a fault condition, the bus is "line" and the shorted wire is "load."  Under normal operation, charging current will happily flow "against" the line/load orientation.

Still not sure how to apply this information to the actual hookup of the breaker. A wire comes from X3/3 to 30A breaker terminal labeled ____, another wire comes from 30A breaker terminal labeled ____ to the main contactor. I'm not asking where to place the breaker along the line, but rather its orientation.

Is this a taboo topic? Or maybe I'm just thick and not able to parse the actual answer from all the extra explanations?

Sorry, I did get a bit wordy there...

The circuit breaker should be located as close as possible to the battery contactor, to minimize unprotected wire length.  The breaker's "line" terminal should be connected to the contactor's switched output terminal and the breaker's "load" terminal should be connected to the wire coming from X3/3.