Note that horizontal look has been intentionally used on the design of quite a few maps on Doom I and II, where enemies can more easily hide from the player down on pits or elevated areas and avoid being turkey shot until they can attack the player. It is true that the engine limitations mean the player can still shoot them blind. But if these monsters happen to also be moving around, that is not a good strategy due to the high consumption of ammunition. Particularly on the higher difficulty levels we all like to play.
Both source ports mentioned on Freedoom official website support jump and freelook and I couldn't find an official unambiguous statement anywhere that Freedoom was meant to be 100% vanilla compatible. Note also that to add to the confusion, the video chosen to demonstrate Freedoom under the "Compatible free replacement" heading on the About page, shows the player jumping on a few occasions.
However when actually playing the game, I noticed right on the first map how access to the top of a few crates was designed as to not require jumping. So, I am not sure if I can trust the rest of the game to be designed around the same rules.