Assign value to custom checkbox using get_option()

You can use the checked function for this.

https://codex.wordpress.org/Function_Reference/checked

The value attribute just indicates the value to be saved if the box is checked. eg.

<input type="checkbox" class="custom-control-input" name="my-option" id="customSwitch1" value="1" <?php checked( '1', get_option('my-option'), true ); ?>>