In DIFFZilla, you have the "Next Diff" and "Prev Diff" buttons. In BC the equivalent are buttons on the main toolbar: "Next Section" and "Prev Section". "Skipping" means that when pressing "Next Diff", it will skip any of the "unimportant" blocks to go to the next important difference section.
In BC, with "Minor" off, sections that have unimportant diffs (comments and spacing) are marked in blue. Sections that have important diffs are marked in pink - I like the different colored sections. The equivalent in DIFFZilla of "Minor" set to "off" is to not use Sourcediff, in this case, both important and unimportant sections are both marked in the same color (red), with no differentiation. I like that I can see the difference in BC. Only with Sourcediff set to ON in DIFFZilla will I see the unimportant sections marked in a different color (green), then they will get "skipped" in "next/prev diff".
With "Minor" off, when I click on BC's equivalent of "Next Diff" or "Prev Diff", I go to the next diffed section, no matter whether it is blue (unimportant) or pink (important).
With "Minor" on, the unimportant sections are not shown, so instead of blue, BC doesn't highlight that it is different at all. So when clicking on "Next Diff", it will skip past the blue (unimportant) sections.
For example, if diff section 1 is important (pink), diff section 2 is un-important (blue), diff section 3 is important (pink), if I'm currently at section 1 then if "Minor" is "off", clicking "Next section" will take me to section 2. But if "minor" is "on", clicking "Next section" will take me to section 3, as diff section 2 is no longer highlighted, so diff section 2 is "skipped" - this is what I meant by the skipping.
With DIFFZilla, if I want to do the equivalent of pressing the "Minor" button in BC, I have to close my diff and restart it with source diff the opposite way. But with BC I can just click on the "Minor" button, don't need to close and reopen my diff session.
Also with DIFFZilla, I get a confusing message about having a read only copy of file 2 in order to get source diff. So this means I can't edit file 2 then in DIFFZilla with sourcediff turned on? In BC I can edit file 2 with "Minor" on or off.
In DIFFZilla, with source diff turned on, I still see a highlight (in green) that the "unimportant" section is changed, although it does get skipped with "Next Diff". But in BC with "Minor" set to "off", there is no highlight marking it anymore, so I'm not distracted by unimportant sections when I don't want to be. I don't want unimportant sections highlighted when doing the equivalent of "Minor" set to "off".
Also in BC, the red and blue markings use the background color of the entire text section, and the actual text differences are highlighted in a different color. In DIFFZilla, only the text characters that are different are highlighted, not the background color.