I don't disagree that Scholar is by far and away more powerful than the other two healers. But I want to tell you that the reasons you've mentioned on why scholar is unbalanced are all the wrong reasons. It's really all about the fairy.

Indomitability *does* come at a steep opportunity cost. It costs an aetherflow stack. You only get three of these every 45 seconds, and it has to compete with other tools in Scholar's own kit for usage. If you use Indomitability, you do not get one of :
Energy Drain
Sacred Soil
Excogitation
Lustrate

Perhaps the LARGEST opportunity cost here is the Energy Drain, because it does damage and restores the scholar's MP.
Indomitability is NOT the strongest heal in the game. The strongest heals in the game are actually the more situationalized ones. Whispering Dawn (again, the fairy is the most OP healer.) is the actual best heal in the game. 100% Free, and the Scholar does not even have to use an oGCD to use it. Given the nature of the game, this HoT will usually be able to do any job without any raw healing numbers required. Assize, while not as strong, also comes with the power of *doing* damage instead of taking damage away. If it can cover something, it is the best for the job hands-down. Earthly star is a little harder to use than Assize, but the same thing to be said here. Because it ALSO does damage, it has no opportunity cost.
When I am making a healing map with my co-healer, this is the priority for when all cooldowns are available and all cooldowns can do the job, in order:

Earthly Star
Assize
Asylum
Whispering Dawn
Collective Unconscious
Indomitability

As you can see, indomitability is more of the "Fall-back" option when nothing else is available to do the job. Yes, it's versatile. Yes, it's good. But it's not OP by any stretch of the imagination. It is actually the worst tool of them all, but gets used the most because it's the easiest to use, and is the most often available to use.

I will also argue that Scholar DOES have to clip and weaving opportunities are NOT unlimited. Bio II is once every 30s, Miasma II costs a TON of MP, and Ruin II is TOO WEAK to weave with. Ruin II is weak enough that even if you were to clip your GCD twice for Off-GCDs, it was better to clip than ruin II. Because Broil II is that much stronger.

Regarding Scholar's personal DPS... well. Because of the aforementioned opportunity cost of Indomitability, Scholar actually ends up doing less damage than both of the other healers when playing optimally. The damage calculations you are probably looking at are attacks on Striking Dummy, where Scholar can use all of their Aetherflow on Energy Drain. Along with the lack of Energy Drain, they lose Miasma II weaving opportunities. When they can't do this, their DPS takes a nosedive. In-content is much different for Scholar.