When speedrunning the game with llcooldave, we found out that megaton has way more clipping bugs than eduke does.
Some bugs are a lot easier to perform than they normally would be.
eduke is similar to dos duke from what I remember, same success rate with clipping.
The only main difference we found with eduke when compared to DOS was this
My link
I recall TX mentioning that eduke handled player being inside a -1 sector differently, outside of play area that is. I could remember it wrong. I recall it actually being some kind of an oddity in the original code that was fixed.
This only seems to apply in to underwater clipping, elsewhere this doesn't really happen.
Anyway, you still clip inside on all versions, the difference is that which one ends up killing you as well.
Duke is very VERY buggy by nature, once you start actually running the game, you will suddenly notice how absolutely broken the game is. Megaton just made things even easier.
Btw, you can also reach the red room trough the arcade with careful timing on movement and jumping in to the spotlight that rotates, you can also make it back to the arcade easily.