I do not see support for this assumption. I think tjhy're aware that PCs will not have these abilities in every encounter, and need to give some thought as to whether they want to use them or hold them.
Let's take a pretty basic situation as an example: The PCs encounter a cave in the wilderness. There are a couple goblin guards standing outside. The PCs can take those guards out if they get the jump on them and then make their way into the caves. Is it worth using some of these 'once per short rest' abilities to make sure you get the jump on them, or do you want to save those abilities for fights against whatever is inside the cave?
If they assume you'll use the ability every combat, you get into the 4E problem where every battle is the same series of attack combos over and over and over... that adds complexity, without really providing diversity. If you're going to be doing the same things over and over, you might as well make them simple so that they go smoothly.
You're right that longer short rests make for more of a resource management minigame, but the problem is that if you only have 1 or 2 short rests a day when you're having 4 or 6 encounters, then those classes are coping with vastly fewer resources than the other classes that rely on daily or at-will abilities. At level 4, you can have a situation of a cleric being able to pick and choose between 7 different daily abilities and cast them in any combination 7 times, plus the benefit of their channel divinity encounter ability. A fighter in the same boat has 2 encounter abilities. Preserve Life is a far better encounter power than Second Wind, and Hold Person or Spiritual or Bless or any number of other spells AND the flexibility in casting those spells is a hell of a lot better than Action Surge's ability to make another attack. But assume they're equal. Hell, assume that 1st level spells aren't as valuable as making an extra attack on your turn, say they have only half the value. Say that the cantrips are absolutely worthless.
That means that the fighter starts with 2 points a day and gets 2 more each short rest. The cleric starts with (4 1st level spells, 3 2nd level, and Channel Divinity) 6 points each day and gets 1 more every short rest. In order for this resource minigame to make sense, then after five shorts rests, the fighter has 12 points to the Cleric's 11. Anything fewer than that and the fighter gets fewer points. Any more and the advantage of being able to keep going after a short rest starts to pay off.
If you have 2 rests a day, the fighter has 6 points to the cleric's 8. That means that even with all these assumptions--cantrips don't matter, 1st level spells aren't as good as attacking, action surge can compete with abilities that simply break the rules of the game--the resource tacking and decision minigame is busted.
That's not to say that 2-minute short rests are going to fix everything. Definitely not. All I'm saying is that the design on the short rests is kicking some classes when they're down. You're giving the players the option of "I'll give you 100 dollars a week, whether you work one day or seven" vs "I'll pay you 15 dollars a day, but you'll work between one and seven days." Sure, getting 15 dollars a day means that you're getting 5 extra dollars a week than the other guy, but that's ONLY if you get to work each day. And your seven days of work is still only slightly edging out the other guy's one day of work. Which sounds like the better job?