I use Mod Conflict Detector and Sims 4 Tray Importer (which has a locate conflicts tool). They pretty much report the exact same things.
Which means you are absolutely right that sometimes what they report is not an actual problem. That's where it helps to actually know and understand all of the mods that you use, so that when you look at the conflict detector report you can investigate more deeply those specific instances which are more likely to be real conflicts.
Even then, though, typically it's not going to cause much of a problem in your game. When two mods both adjust the same tuning file, for example...one of them wins. Often they will have the same changes too, which is where the creators saying they do not conflict even though the tools report that they do can come in.
When the detectors report a problem that I'm unsure about, I'll generally open both mods in Sims 4 Studio and look at what each of them does and which game files each of them alters. To get an understanding of what the conflict is, if any. Sometimes I'll merge the two mods and make my own custom mod that combines them if there is true overlap and that overlap isn't the same.
When in doubt though, following the community to get conflict information from others and doing your own playtesting is all you can do. The conflict detectors don't detect conflicts in script mods at all, so that's actually the main tool I use in the first place.
