crl22191 wrote: it seems they indicate completely different points of bonding the neutrals and grounds, the first in the trough, the second in the individual disconnects.
Why is this difficult? The neutral wire is the bonding wire at all places along the service until you hit the main disconnect(s). Your neutral will be bonded the chassis in the meter enclosure, the trough, and in both disconnects. The trough is not a disconnect, so there is no need to isolate the grounded and grounding wires yet. The GEC is attached to the neutral in the trough because it is the only neutral large enough in this example. If a larger neutral (2/0) was run to one of the disconnects, the GEC could have been connected there which may make people feel more comfortable.
Yes, there will be current flowing in the metal service raceways, troughs, and enclosures, but this is how most service equipment is.