Probably not what you want to hear, but you have figured out the behavior - the buttons only control whether triggers are sent to the TRIG output - they do not cause steps to be skipped. SEQ 3 does not have a function to cause a step to be skipped and advance to the next step. You can only skip steps at the end by reducing the number of steps, or by sending a trigger to the RESET input. You cannot skip steps in the middle (at least not by using any functionality built into SEQ 3).
Unfortunately the SEQ 3 documentation does not fully describe all the functionality, so it is not surprising you are having some problems and misunderstanding. For years it did not have any documentation at all, so incomplete is better than nothing.
Before there was any documentation at all, I did extensive experimentation with SEQ 3, and developed some unofficial documentation that is much more complete than the current official manual. I can’t promise that nothing has changed since I wrote that documentation, but I think it will give you a much better understanding.