As was mentioned, not all balancers are the same, and more important, neither are their operators. Most machines have a +/- .3 switch, which will tell the operator "ok" if within that range. Okay for some cars, NOT any Honda procuct I have ever seen. When I bought my Hunter DSP9000 balancer, I ordered it with switch deleted. They must be balanced to 0/0
Where the weights were placed depends on how the machine was set. Most modern balancers have at least 2, if not 3 settings for plane. If set for 'dynamic' you get readings for both outer rim placements. If set for 'static' you get a single plane, single weight placement, designed for outer rim only. Mine has an addl set setting for centerline single plane, designed precisely for tape weights on alloy wheels.
And the reason it comes and goes is quite simply, harmonic imbalance. The harmonic disturbance is strongest at a specific speed. Alignment can never cause a vibration, nor can brake rotors- unless you are braking when you feel it.
However, if your wheels are NOT hubcentric, its all a waste of time. You will never gets these balanced properly.
HTH,
MB