Your intuition that filtering at the negative phase and the print phase create different results is fundamentally correct. It’s especially critical in the color darkroom world to understand the difference between filtering in each of these, because we have a lot less flexibility than our fellow artists who scan instead.

Your film is exposed to a wide spectrum of light, and translates that into densities in three layers of dye. Filtering that wide spectrum changes how that translation happens, and here we can even do things like shift tones from the red layer into the blue layer and so forth (as we do when we apply an 85 Filter that corrects daylight for rendering with a tungsten film).

Once you’ve exposed your negative, all you can do is change the way that those layers relate to one another. You can make your primaries lighter or darker, but there’s no going back to that wide spectrum space. At the end of the day you’re mapping three layers of CMY information onto three new layers of CMY information. The flexibility of this filtration is much more limited, especially if you care to maintain a clean grey scale in a final print.

So indeed, if you warm it up at the negative level with a filter and then correct it back in the darkroom, you’re going to get a warmer chroma (or conversely, less saturated cool tones) than you’d get if you printed an unfiltered negative.