The colors in the weight painting mode are analogs of the numerical values use to determine the influence of a selected bone on the mesh, so in that sense they “control” the mesh influence, yes. But always remember that the colors only represent numerical values, and how these numbers relate to one another from bone to bone can make a difference in how things work.
This is how I understand the process:
The weighting numbers are both relative and normalized for each bone – relative in that any one bone’s influence can be modified by another bone’s influence, even when a numerical weight stays constant. Example: A set of vertices in the upper torso may have influence from one or more spine and neck bones, the clavicle bone, and the shoulder/deltoid region bone. If the weight is changed for any of these bones, it can make the effective influence of the other bones somewhat different even though their weight numbers may not change. The other side of this coin is that if the verts are influenced by only one bone, the effect of the lower values will be relatively greater – this may have something to do with your situation.
A practical example – in weight-painting some areas of my “Katrice” mesh for Kata, I often would apply a very small weight, on the order of 0.0625, to a vertex that has only very small influence(s) by another bone, and that vertex would suddenly be displaced rather far by the small additional weight. In a sense it’s always a balance between opposing weight influences, in some ways like muscles opposing one another.
“Normalized” means that for any one bone the weight on a vertex will always be in the range of 0 to 1.00. But in a sense this is kind of misleading in that afaik all the influences on any one vertex cannot add up to more than 1.0 (also “normalized”), so if any values are “in the red” they will swamp influence from other bones. This is useful in a few fairly limited situations – usually any one bone’s influence should be less than 1.0. But again the complementary effect is that when only one bone influences a set of vertices, all the weights will have a strong influence on the deformation.
Again an example: Say the verts of five edge loops in a torso mesh (roughly cylindrical) are given a weight of 0.25 for a bone labeled Spine. Of these, only the verts at the “outside” of this mesh regions, loops 1 and 5, have any influence from other bones. That means Spine will completely control the deformation of the other three loops of vertices, even though the weight is much less than 1.0. There is nothing else to influence the mesh deformation in that area.
Again, this is how I understand the weighting to work, based mainly on my experience doing it. The technical details may be somewhat different than I’ve described but these are the effects I’ve observed.
The upshot is to make sure you have a balance of influences on any one set of vertices.