What you see
isn't what's saved.
The theme holds the defaults
Every visual starts from the report theme: Desktop's base theme, plus any custom theme on top. The visual's file doesn't repeat those values. It records only the settings where this visual differs from the theme.
That keeps files small. It also means a setting you can plainly see in the Format pane may have no line in the file at all.
Change a setting, watch the file
In the seed, the card's padding was set to 4 px. Desktop showed an Individual padding switch, and it was already on.
Predict first: you leave Individual padding on, which is the theme's default for cards. What does the file record for that switch?
Three things that follow
This is why the agent copies only what Desktop wrote, and never "completes" a block with settings it thinks belong there.
The rule, in one breath
A file records differences from the theme, not the settings you see.
To teach a setting, the seed value must differ from the theme. To read a seed, remember that what's missing is set by the theme, not forgotten.
Next: the steps for changing the seed, in order.