The windows version is specifically a port of Nanosaur Extreme, which is an edition of Nanosaur featuring more enemy spawns and pickups than the original. Listed here are comparisons between the original (as played on original hardware) and Windows, but currently no comparison with the Mac OS version of Nanosaur Extreme.
Differences that have speedrun implications: Enemy spawn distributions are different, of course. For example: Some enemy spawns which are reliably found in the port are not in the original, and in the original, there is a much higher population of Dilophosauruses in the area with Pterosaur eggs (the final area in the current best speedrun routes). The falling rock spawns are not quite the same, and you cannot rely on the same timing to get through that area without incident. Various audio cues (t-rex walking, pterosaur wing flapping, fungus exploding) are unreliable or even absent in the port. The time between pressing the button to start the game and the actual beginning of the game is practically absent in the port, but very significant in the original! The original is more prone to slowing down. The timing for the double jump at the tall mound to get full items at the beginning is significantly tighter in the original. In the original, walking into a portal while holding an egg will collect the egg automatically. This behaviour does not seem to work in all installations of the port. However, for speedrunning purposes, it is currently more useful to throw all of the eggs from as far away as possible, in order to save time.
Differences that may or may not have speedrun implications: The Sonic Scream weapon is not supposed to be invisible like it is in the port. The minimap is not supposed to flicker obnoxiously like it does in the port. Someone has managed to get the port to play the cutscenes fully (not just the audio), but I have only seen one instance of this and have no idea how it was achieved. You can't remap your controls in the port! And the default controls are not the same, because of different keyboard layouts. Fade transitions between screens are absent in the port. In the original, if you are holding an egg when you die, the respawn portal does not collect it. However, you can get this to happen sometimes in the port.
Important things that are NOT different, but you may have been wondering about: The respawn portal does collect eggs that are lying on the ground if they're directly under it, in both versions.
