Yes, of course you have to use some judgment and avoid doing extreme things if you set the action with the trussrod. But for minor tweaks it's perfectly safe and much quicker than fiddling with all your saddle screws and having to reset the radius and all that. I'm sure that's why the Ernie Ball guys recommend this approach.
And I disagree that saddle height and relief have to be changed together. I'll bet everyone here has adjusted their saddles at one time or another (and probably many times) without feeling the need to adjust the rod, and gotten good results. I know I have.
It seems counter-intuitive and maybe even a little sinful to use the trussrod alone to adjust the action, but there are two reasons why it works:
1) There is a range of acceptable relief settings.
2) Small changes in relief have the same effect as large changes in saddle height.
The result is that the truss rod can have a broad range of effect on the action while staying inside the limits of acceptable relief.
Here's a quick and dirty graphic to help visualize...
It shows two things at once: 1) the relief required for a given action, and 2) the saddle height required for that same action while leaving the neck straight. What you see is that it takes much less relief to create a given action than it does saddle height. If this drawing is anything like right (and I'm open to peer review on all of this), the ratio of the effect of saddle height to relief is about 1 to 3 .
Keeping the 1 to 3 assumption, this means is that adding or subtracting 1mm of relief is equal to moving the saddle height 3mm in either direction, which is 6mm or about 1/4" of total range. Since most bridge saddles only have a range of about 1/4", you can see why adjusting the relief works: all it takes is a tiny amount of adjustment to cover the whole range.
So if you can live with about +/- 1mm of change in relief, which most people probably can, then you should be fine adjusting your action with the truss rod.
The big caveat is that the truss rod method is for adjusting a bass that's already been properly setup, not for doing the initial setup. IIRC this is what the Ernie Ball FAQ is referring to when they recommend the truss rod method -- adjustment, not initial setup.