Agreed, however, when you compare both the Laserdisc and the DVD, if you overlay them both over each other in a side by side comparison (something I did in iMovie as a test), the laserdisc goes out of sync with the DVD very quickly. So yes you are right, the film was not “slowed down” or “sped up”. The film just gained and lost some frames in some shots on the film out. So yeah, it was rendered frame by frame for standard 24fps projection, its just that when Pixar were processing the film for celluloid, the Avid Video Composer caused the movie to gain and lose a frame in all of the shots.
That’s not how it works, the digital format doesn’t have a frame rate. You render it out to a series of images which has no frame rate, it’s just 0000001.dpx, 0000002.dpx, 0000003.dpx and so-on, there’s no way for it to gain or lose frames in that process. The printer doesn’t know about frame rates, or for that matter audio - all it knows is that it prints frame after frame to a negative that then gets processed, and then a colour-timed interpositive is made later to strike prints from. The DVD and Laserdisc won’t be a definitive source, they are many reasons they may not have the same frame counts as they may have been edited on tape (they probably were) we’re talking about editing together a 10 reel movie, potentially adding subtitles or text over the image especially for 4x3 where credits or other text may be cropped out, potentially doing a scene-by-scene colour correction and editing it back together as well. Plus I don’t know what print they used when they made them, for all we know there were random lab splices in it that had to be removed physically, or it had other repairs made with frames removed.