Another problem as an academic is that you don't always have the space to go into all the results, and unexpected side effects might not make it into the abstract or the title so they would quite possibly not be picked up by others looking for that topic. Writing about the unexpected side results in another article might not be enough to get it published etc. etc.New info could be added without changing the primary outcome. Same with biomarkers. Negative side effects should already be covered inderectly by adverse events. Positive side effects could be added as secondary or tertiary outcomes.
As a silly example: if you studied viagra, the primary endpoint should be hypertension and pectoris. But during the trial, you discover that it helps with erectile dysfunction. So you report a negative result for the primary endpoints, but include a section about the unexpected side effects. That’s just reporting everything you found.
That can obviously be valuable. On the other hand, changing the primary endpoint after the fact would require very heavy arguments. And going by what I’ve encountered so far, very few studies that change endpoints have valid reasons to do so. It’s mostly about getting a result, because publishers and employers don’t want null-results. Or the researchers don’t want to be wrong.
In my field (epidemiology) a reason to change the outcome or analysis method can be that the data collected is not good enough to follow the original plan. I've spent years to get data from health registries, only to find that they are not all that they are made up to be, and back to the drawing board to figure out if they can be used for anything resembling what we were supposed to do.