The difference is that this affects a vote that was held before it passed.
I understand what you are saying, but in IL that wouldn't matter. The ruling is that it is not the vote that is protected but the office. Once a referendum passes, the office is changed. Since the officer is not yet sworn in when the office changed there was nothing to protect by delaying the impact of the referendum.
For instance, let's say there is a referendum to eliminate the office of County Coroner at the same time as an election for Coroner. The votes would be certified for both offices at the same time. The referendum has then eliminated the office, so when it comes time to swear in the elected Coroner there is no office, so no one is sworn in.
The same thing applies to the creation of an office. For instance, if there is a referendum to create a Park District, there can be an election at the same time for Park District Commissioners, even though there may be no elective office at the time of petition filing. If the referendum succeeds, then the results of the Commissioner races matter, and those who were elected can be sworn in.
One interpretation of the CO referendum is that it both eliminates and creates offices at the same time. It eliminates electors for the statewide winner and creates offices of electors for candidate who receive suffient votes in proportion to their vote. With this interpretation, the referendum binds the office before the electors are sworn in, so it would be effective in 2004.