I think fighters with a higher health value normally take more damage, while the lower health characters take less damage. I don't think the Defense stat is more-or-less irrelevant: I believe the Defense stat determines how much damage a character receives, separate from the Health stat.
According to what I see on GunFrame, (an app that has a copy of frame data and stat information from the game, the app is available on iOS and Android,) the standard for non-superhumans is 1250 health and 1350 defense. The standard for superhumans: 1050 health and 1500 defense. The mix: 1150 health and 1450 defense; (it applies to Blue Beetle, Robin, The Flash.)
Black Canary & Cheetah: 1200 health and 1350 defense.
Supergirl & Cyborg: 1100 health and 1450 defense.
Darkseid: 1400 health and 1150 defense.
In the following video, I test a Red Hood combo (3,2xx4, 3,3,2,1+3) on four characters.
(Hyperlink in case the embed doesn't show.)
The Flash: 1450 Defense, 1150 Health.
Cyborg/Grid: 1450 Defense, 1100 Health.
Black Canary: 1350 Defense, 1200 Health.
Batman: 1350 Defense, 1250 Health.
As you can see in the video, Flash and Cyborg/Grid received the same amount of damage despite having differing max health; Black Canary and Batman also received the same amount of damage even though their maximum health is inconsistent. If the Health stat was all that mattered, they should have taken slightly different damage totals. By this evidence, I believe that the Defense stat is what determines how much damage is received.
However, this does not nullify what you said about overall health in competitive mode being the same aside from a 1-to-3% difference. I think that the aforementioned standards of high health/low defense or low health/high defense are the reason for things being pretty much the same across the cast. (Should look into the odd pairs, tho.)
And yeah, I agree that things would be much easier if we had consistent percentages instead of the current form of damage calculation; which I assume is better suited for the non-competitive mode gameplay with gear stat boosts and all.
It still doesn't matter, that's why I keep saying whatever number this is, divide it into the HP.
Flash and Cyborg receive the same numbers but it isn't the same percentage. The damage number itself is more or less irrelevant.
241.40 was the combo done on those two.
241.40 ÷ 1150 = 20.99 or ~21%
241.40 ÷ 1100 = 21.945 or ~22%
Now go into practice options, go to the Health value where you can alter it from 1% to 100% and set it to 21% for Flash, and then 22% for Cyborg. The value on the health bar should both be very close to 241.40 but as you can tell, the percentages are different.
Anyone sharing the same HP will receive the same damage in percentage, which is the actual damage. The large numbers of 458.69 or whatever are more or less dummy numbers and don't correlate anything really between characters. It's just the number to divide into the HP to find out the actual damage. It doesn't matter if it's the same for every character, once converted to percentage through each specific HP value, thats when you'll see the true damage.
All in all, it's such an unnecessary process and nonsensical numbers when they're so close to one another in standard percent.