Often, designers project our websites using tools such as Illustrator, Sketch, etc., and designers try to keep in mind the grid that the developer will use to best convey accurate measurements to the developer.
Grids are often implemented in the following order:
- Margin (optional)
- Column
- Gutter
- Repeat 2 and 3
- Margin (optional)
After adjusting the grid in the tool, the developers will try to place the blocks in the grid system, starting from the column and NOT from the gutter. As below:

However, in Bootstrap v3, some elements occupy the width of the gutters, and therefore this may be inappropriate and leads to confusion in the proper design for these websites. In the example below, this is the input to the form. Pay attention to how the entry begins, and includes a 15px slot for gutters (twelve .col-xs-1 with a slot inside to indicate borders are inserted). Codepen link
.col-xs-1, .col-xs-3 background-color: blue .col-xs-1 span, .col-xs-3 span background-color: pink .form-control background-color: black !important`

However, in my design, I tried to start with a column, as shown below (columns are indicated by a space in GRAY, the columns are simply thin due to responsiveness, but the gutters remain the same size for the iPhone 6 Plus).

I do not understand something? As I design and develop the product myself, I'm not sure how I can get accurate measurements in Bootstrap for these elements that contain the groove in the design, and then develop it in accordance with the design. How do I create a Bootstrap grid when some elements seem to occupy the width of the gutter? Or, conversely, how do I change Bootstrap code so that some elements DO NOT accept the width of the gutter?
TYPICALLY elements accept the width of the gutter? If so, why should designers design from a column?
(PS I know there is a Stack Exchange project, but I feel that this issue may arise due to a misunderstanding of Bootstrap, not design principles)