Correct. You absolutely DO NOT want to equalize out your equal loudness curve. That curve set is built into human hearing, you don't want to equalize it out, and besides, it's level dependent.
The curve you'll get from this test will be the equal-loudness response of your own hearing with the mask of the response of the headphones/IEMs you used for the test. The results are pretty meaningless and not useful at all for setting an equalizer. At best the results present something that is of interest to look at.
The target response curves of the three types of headphones plus IEMs are all different, but none are flat, and certainly none are related to the equal-loudness curves. Headphone target curves are there to compensate for the difference in the way sound is presented to the hear by headphones vs a free field.
You can experience highly accurate and detailed headphone EQ with the Audyssey "amp" app, and some of the others. Audyssey also features their dynamic EQ, which compensates for the effect of the change in hearing response at low levels relative to the spectral balance at the level at which music is mixed.
Using an equalizer to compensate for an individual's hearing difference is also not a great idea because every individual has a build-in established "normal" based on every-day hearing. Attempting to compensate for a deficiency, unless large enough to be considered a hearing loss, will always result in unnatural balance because of its contrast with what's heard in life. It's for this reason that people who have hearing aids prescribed are encouraged to use them all day, every day, or they will always sound "wrong".
Consider going to a live performance. If during this performance, tones where reproduced for the audience, the different frequencies will be perceived with different loudness levels (as illustrated by the loudness contours.) Does that mean that one needs to somehow equalize a live performance, or for that matter the entire world, to "correct" for loudness levels? I don't believe so.
The job of a high fidelity audio reproduction system is to reproduce a live performance, or a particular set of effects, as close as possible to the original source. This implies that the lumped sound system frequency response should be as flat as possible so as to "get out of the way."
If equalizing using the loudness contours, what will happen is that a violin or any other instrument played through the equalized rig will sound substantially different than a "real world" violin or any other instrument.
Sure.... but if you make the headphones produce an equal balance curve, then in terms of absolute energy (as measured by energy output) reconstitute the equal loudness curve? In my mind, that would be getting the headphones "out of the way". And I know it's level dependent (as shown in the ISO curves above), I can't control for that yet, but I'm sure I could figure it out. Replaygain would be an interesting first step to get a global range value to work from.... I'll check out the Audyssey application.
As far as personalizing curves.... headphones are personal enough so if I personalize them to me.... that's not exactly a bad thing :-). Besides, sounding "right" or "wrong" is dependent on the coloring of the headphones anyway....
And in more practical terms, I don't think that it's physically possible for a headphone to accurately reproduce live frequencies because beyond a certain frequency low point, the actual sound pressure will decay off a headphone faster than it would on a speaker (or live, for that matter).
In terms of live performances.... the microphone doesn't impart the equal loudness curve. Our auditory systems do. So the live performance wouldn't be corrected at all.