Briefly, this mode allows you to calculate an "across-all-cycles" illumination correction function on-the-fly as part of a pipeline you're then going to use it in, rather than running it as a separate pipeline. As a convenience function, I get why this was made, but I'm going to argue it's actually bad for 3 reasons:

1. It's one of a very few modules that complicates "how does CellProfiler behave" substantially by not just doing normal "act in a linear fashion, with maybe remembering some stuff from a previous cycle" ; I'm not sure whether we could actually simplify the underlying source code if this no longer existed (since I believe one or two other modules do things like "use the minimum intensity from across the whole cycle", though I'd also be fine discussing deprecating those), but there's a non-zero chance.
2. Ultimately, it takes longer to run in the grand scheme of things, because how many times do you really run CellProfiler exactly once and only once without EVER adjusting any of your parameters? Maybe other people are better at doing this than I am, but I feel like the vast majority of the time I run pipelines once, tweak, then at least one more time, so you're double- (or more) calculating this.
3. It harms reproducibility - with a "normal" CellProfiler pipeline, if you give me one Group (whether that's one or many image sets), on another computer I should be able to exactly (or to within rounding errors caused by different OS libraries, anyway) reproduce your results. Pipelines with this enabled ultimately are NOT reproducible, because I need to have every Group you did when you ran it in order to get the same result, and/or when you yourself run it multiple times and change your image sets (adding more or dropping one you realized was bad), your own results will change, but silently-to-you.

Thoughts? Any lovers of this mode want to speak out for its continued survival? Since we're removing a functionality, I would say "announce in CP5 that will no longer exist in CP6" would be a reasonable deprecation schedule, given our "major release every ~3ish years" schedule we've been on recently, but others can argue for something else.