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This bug effects also affects other explosions in the game, such as TNT explosions. It doesn't affect bed and respawn anchor explosions (because their damage source is specified as a BadRespawnPointDamageSource with scaleWithDifficulty = true) and creeper explosions (because it dies and the causingEntity is null).

Code Analysis (yarn mappings):

Scaling damage with difficulty is done in the damage method of the PlayerEntity class:

public boolean damage(DamageSource source, float amount) {
    ...
    if (source.isScaledWithDifficulty()) {
        if (this.world.getDifficulty() == Difficulty.PEACEFUL) {
            amount = 0.0f;
        }
        if (this.world.getDifficulty() == Difficulty.EASY) {
            amount = Math.min(amount / 2.0f + 1.0f, amount);
        }
        if (this.world.getDifficulty() == Difficulty.HARD) {
            amount = amount * 3.0f / 2.0f;
        }
    }
    if (amount == 0.0f) {
        return false;
    }
    return super.damage(source, amount);
}

Whether the damage is scaled is determined on if the scaleWithDifficulty field of source is true. In the damage method of the EndCrystalEntity class, these two lines handle the explosion:

DamageSource damageSource = source.getAttacker() != null ? DamageSource.explosion(this, source.getAttacker()) : null;
this.world.createExplosion(this, damageSource, null, this.getX(), this.getY(), this.getZ(), 6.0f, false, World.ExplosionSourceType.BLOCK);

In the case of TNT lit by a player, it explodes without specifying the damage source, instead having a getCausingEntity method that is called in Explosion.getCausingEntity which is called in DamageSource.explosion which is called in the Explosion constructor called in World.createExplosion.

In both these cases, DamageSource.explosion is called:

public static DamageSource explosion(@Nullable Explosion explosion) {
    return explosion != null ? DamageSource.explosion(explosion.getEntity(), explosion.getCausingEntity()) : DamageSource.explosion(null, null);
}

public static DamageSource explosion(@Nullable Entity explosion, @Nullable Entity attacker) {
    if (attacker != null && explosion != null) {
        return new ProjectileDamageSource("explosion.player", explosion, attacker).setScaledWithDifficulty().setExplosive();
    }
    if (explosion != null) {
        return new EntityDamageSource("explosion", explosion).setScaledWithDifficulty().setExplosive();
    }
    return new DamageSource("explosion").setScaledWithDifficulty().setExplosive();
}

Because both attacker and explosion are not null, a ProjectileDamageSource is created which extends EntityDamageSource which overrides the isScaledWithDifficulty method in DamageSource.
Instead of

public boolean isScaledWithDifficulty() {
    return this.scaleWithDifficulty;
}

it's

public boolean isScaledWithDifficulty() {
    return this.source instanceof LivingEntity && !(this.source instanceof PlayerEntity);
}

This is done to have difficulty scaling apply only to mobs and not players. Since a player lit the TNT and a player hit the end crystal, this will be false, so the damage of the explosion will not be scaled.

Proposed Fix:

Change EntityDamageSource.isScaledWithDifficulty to

public boolean isScaledWithDifficulty() {
    return this.scaleWithDifficulty || (this.source instanceof LivingEntity && !(this.source instanceof PlayerEntity));
}

This shouldn't break anything to my knowledge.

Edit:

Because of MC-258561 and MC-157206 it's probably better to create a separate damage source for explosions instead of using the one for projectiles.