Because those controls don’t use the less variables you modified. They either use other variables or don’t use less at all. The styles of the selectize widget for instance are loaded from a WebJar as plain CSS so yes, they are not affected by your change.
Overwrite the padding with CSS, using more specific selectors.
The selectize widget comes with a less file that uses Bootstrap variables, but the problem is that we don’t have yet support for evaluating a less file loaded from a WebJar (in the context of the current color theme). So we load instead the plain CSS file for now.