"That only one thing didn't work doesn't refute the grandparent comment's point. They pushed the boundaries in lots of areas and of course most succeeded..."
It does. The risk was purely commercial, not technical. The commercial risk was that they'd have to do too much redevelopment to get the aircraft certified and flying and run out of money. By and large the design is OK (apart from the battery), flies, and has the required performance. Once the snagging list has been dealt with it looks like it will be a fine aircraft. In that sense it turns out that it wasn't risky at all.
"A 1% risk of a battery problem sounds manageable but if there is also a 1% risk of an engine fan blade issue, a wing strength issue and dozens, hundreds or even thousands of other issues then sooner or later you might be talking real possibilities or even probabilities of something going wrong although you don't know which."
Only if you ignore them. The point of development testing is to establish that all of those components do indeed meet their specification and are not in fact a risk to the project. You deal with risk in a project by identifying areas of concern and work on them early on. That way you either kill the project before you've wasted a lot of money, change the design or find that the risk didn't materialise. Flight testing is there to make sure that the specifications themselves are correct. Certification testing and inspection is there to make sure that the rules have been followed and that no detrimental technical risks remain.
In the case of the 787's battery it is highly unlikely that any of the companies have taken short cuts in manufacturing or testing (the reputational damage would be immense, and could potentially attract jail time if there were a bad accident). Thus far the NTSB, FAA and everyone else seems baffled as to why the batteries are failing, which suggests that the rules and specs have indeed been followed.
This in turn may suggest that the behaviour of Li-ion cells isn't understood well enough to be able to write a correct specification in the first place. That's no one's fault; the writing of the specification for the battery is something that has rightly involved the companies and also the FAA, EASA, etc. What more could be done?
If the ultimate conclusion of the inquiry is that the spec is wrong then Boeing will have to change battery chemistries, or back off on the specification somewhat (larger, lower power density, greater margins all round). If I were in charge I'd be sorely tempted at this point to change chemistries and accept the weight penalty.