In the chapter Welcome to Black Mesa, Shephard finds himself above a room flooded with radioactive waste, which access is forbidden as long as the Loader below is working. The Loader is blocked by stored crates that Shephard must destroy with a bullet (or a grenade) to allow the robot to proceed and clear the access.
As the following elevator leads to the same part of Sector C Line where the second Loader is seen in Half-Life, it is likely the two Loaders are the same individual. Of note is that between Freeman's and Shephard's passing through that area the leak seem to have been repaired, and probably by human hands. The Gearbox developers also did not change the Half-Life tram position.
The model has animations not seen in-game. They include "run", "heroidle" and "herodie". It was probably to be seen destroyed at some point in the game's development, likely in a scripted sequence, as "herodie" shows it in parts after a small run.
The crate is part of the model and is placed under it when not in the animation, so that it is out of the view of the player. The Opposing Force model is identical except for the crate, which is a green metallic one instead of wooden.