Many thanks to the author of the article, I have definitely learned some new tricks with my 5Dm3. Completely coincidentally I started practising with bird shots a few days ago (with my zoom lenses though), as pretty much by accident I captured a couple of really nice BIF shots last year, and thought I might be time to train that as a skill.
As others in this thread, I am also thoroughly annoyed by the Spot AF metering of the 5Dm3. It just doesn't really work all that well, especially compared to other cameras. A dark bird against an overcast sky will always result in a dark bird with a grey sky (instead of a properly exposed bird against a bright sky), regardless of any setting I can find. I've noticed the problem dozens of times when city shooting as well. For comparison, both the older 50D and the newer 70D do a much better job selecting the right exposure in similar circumstances. You just can't trust the Spot AF metering on the 5Dm3. If anyone has a working solution or process for this that doesn't involve having the manually adjust settings repeatedly through the shooting session, I'd be happy to hear it.
As for auto ISO, this is quite likely my biggest gripe with the 5Dm3. It is fantastic to be able to limit the ISO to 100-800, but the fastest shutter speed limit configurable is 1/250. With a tele attached for normal shooting I'd already prefer a shutter of 1/500 at ISO 200 vs 1/250 at 100. For action shots, 1/1000 or 1/1600 is needed. You can emulate that a little by raising the minimum ISO to 400 (if the light circumstances are correct), but that is not always ideal (and 400 is the highest minimum value you can set).
Almost every time I use the 5Dm3, I hit one or both of these issues, and at least the latter is easily fixable with a software update - I guess Canon expects me to buy the 1D X for that basic feature. Luckily neither has caused me to miss the money shot so far, but that's a question of when, not if. Canon being the EA of electronics though, I don't expect either issue to be fixed without buying their newest (also artificially limited) camera model for the price of several small cars.
Interesting you have an issue with spot metering. I have issues on the exact opposite end of the spectrum...spot metering often overexposes too much or results in a slower shutter speed...too slow for the BIF shots. Perhaps the issue you are having is due to the object not beig large enough in the fov. Spot is not an exact spot but does tape away from the center. Unless the subject is large enough it will meter on the background. Also note that the 5d3 spot meter does not follow the af point. It is always on the center. The 1dx will follow the af point.
Regarding auto iso... I find this mostly useless for all practical shots except for photos of the family. It could be a viable option on the 1dx for those shooting sports. I prefer to control the iq of the image based on what i am shooting. Fix the iso for the type of shot i am using and use Av mostly. I use the dial on the back to quickly compensate for backlighting or to expose to the right using the histogram.
I generally dont use spot metering except for portraits or where subjects are at least 50% of the frame.