I fail to see how EUD actions are any sort of modding.
1) EUD actions allow the kind of advantage that forces everyone to use them. That is why modding isn't allowed in mapping contests, and mod-allowed contests are called modding contests. This is not the same for EUD conditions, where using them is optional since their impact, especially in multiplayer environments, is almost always negligible.
2) EUD actions cause the map to be unplayable except in single-player, or in limited circumstances at predesignated times. This is the same reason many mappers dislike mods. It greatly limits the audience the map is available to, and heavily restricts the mapmakers ability to enjoy the map himself.
3) The mechanics of how they alter the game is irrelevant, or whether or not they have ever been usable without third-party programs. You have listed a few totally irrelevant differences between EUD actions and mods. Another one similar to those would be "they aren't called the same thing." Well that's great, but the fact is that they still have all the same inherent flaws and disadvantages that mods do.
They're not an unfair advantage.
Not any more than a mod is, assuming the information for modding was readily available.
I'm not about to nix some complex system because an amateur is unable to grasp it.
I'm not about to applaud some system when an amateur couldn't manage it without requiring third-party programs to use it.
Of course, the same logically nonsensical argument could be used to call those who do or do not use mods "amateurs" as well.
Furthermore, EUD actions cannot be written into SCM Draft 2. Do not expect them to be allowed until there is any easy way to implement them, and they become well-documented (much akin to Roy's EPD guide). "In the future," does not necessarily mean the next contest. I wouldn't permit them until they were easily accessible.
You shouldn't permit them until they can be played without modding StarCraft to do so, or you should permit modding altogether.