Hi Paul,
I'll try to answer your questions. This is based on my opinions and is based on what I am doing, but not flying yet. YMMV.
You haven't stated what your aircraft's mission is, but assuming day VFR for fun, I would (and am) building my electrical system using the SD8 for a backup in case of main alt failure. Enough to comfortably get me to an airport. Much lighter and simpler than the 30 amp alt/ 2nd battery config.
Voltmeter and ammeter via the EFIS/EIS will tell me if the backup alternator is keeping up with the demand for power and if not, I can shed more loads for awhile.
I like the avionics switch/relay and have put one in. I think the benefits offset the additional complexity of wiring and doesn't add much weight.
Shorted battery? How rare is that? Just replace it regularly.
I'm using a battery bus for the convenience of wiring. It powers the Pmags, Endurance bus and the horn. Yes, I said horn. Shouldn't every airplane have one? The horn can honk even with the master switch turned off. I think this is a valid safety feature, but it is a relatively heavy item. I'm using a compact motorcycle airhorn compressor combo and looks like this one, see
http://www.twistedthrottle.com/trade/productview/2137/
I feel the aux alternator should be connected directly to the battery so as not to require the contactor to be on when trying to conserve power. Also, the batt bus is connected here too which feeds power to the endurance bus via the alternate feed path. Your drawing is missing this feed path by the way. I don't think it would work any other way.
I believe the diode's typical failure mode is to go open circuit. Ask Bob Nuckolls
My 2 cents YMMV
Bevan
RV7A Z13/8 with Pmags and horn

Not flying yet. YMMV