If an in-ear response measurement is taken with a source at 30 degrees, then the headphone is placed on-ear at 90 degrees but with the eq curve of 30 degrees, my guess is there will be a confusion be a disparity between the localization cue derived from the curve and the cues derived from the inter-aural time delay, or rather lack of it, from the headphones. Perhaps its not a problem, or at least a minor one. It also seems that a single point HRTF would result in a target curve that's right for that vector only, and wouldn't account for other positions in the stereo field. Couldn't find this quickly, but I know I've seen essentially polar plots of ears, and perhaps it's a flaw in memory, but I recall there is a significant difference between between response at zero, 30, and 90 degree angles. Probably in a paper about localization.
I'm not convinced that the pinna isn't a factor in on-ear headphone response, but it's clearly bypassed with IEMs, so that would mean different target curves for IEM vs on-ear. Mostly at the upper end of the spectrum, of course. No sound in real life originates from within the ear canal, so the results of that transducer position would have to be accounted for.
There will be no confusion as there is just no cues from headphones. What you will get is quite loudspeaker-like sound. Granted, the pinna changes the sound and is directional, but as apparently binaural recordings are generally reproduced quite correctly, its contribution is rather small at typical angle for headphone driver.
You don't need many curves to emulate standard loudspeaker setup if you don't need head tracking. SVS Realiser and the like do not dissect the music into a true binaural representation as there's no information about position of source of each sound in the recording, there's just two continious channels which are intended to be reproduced by loudspeakers. What these systems do is emulating loudspeakers using HRTFs, having a set of HRTFs sor one angle would just not allow head tracking, it'd feel as if speakers are pinned to your head on long rods regardless of how you move your head.
A HRTF for emulation of stereo speaker setup consists of four TFs - left speaker to left ear, right speaker to right ear, left speaker to right ear, right speaker to left ear. It's easily measured and there are even some readily availible on the internet with an option to check your compatibility with it.
There's however other nitpick. Headphones are usually designed to partially emulate diffuse-field or free-field HRTF (or some inbetween) so they could present sound at least somewhat similar to loudspeakers without using crossfeed or HRTF system. If you use an obtained real HRTF with such a HP, you'll get a mess of two HRTF overlaid. So either you'd have to use some truly flat headphones (don't know of any really, save perhaps for few Fostex mods) or equalise them back.
So, to get everything equalised, you'd have to do such steps as:
1) Equalise the speaker system. Get an TF of a setup with speakers at +-30 degrees off axis, with mic in center. If you don't have an anechoic room, to get a perfect result you'd have to get 4 TFs, just like a full set of HRTFs - because there could be some room modes present at one ear and non-present at another. Though in most cases, I think, one TF from either speaker to mic placed "inside head" would suffice.
2) Get HRTFs by using in-ear mics, having speakers compensated by inverses of TFs obtained in 1). To get really perfect you'd have to measure at eardrum, I suppose, but again, that does not seem to be practical.
3) Get a headphone TF by using in-ear mics and headphones. Again, to be perfect, it'd be good to measure at eardrum, but it's not practical - there are peaks and valleys in HP's responce which shift around with even slight change of position of a headphone, this is most pronounced in at-eardrum measurements, so such EQ would be practical only if you'd glue headphones to head. That is the part of headphone's characteristics which is not controlled by EQ and that's how real good HP differ from just good ones for one who uses EQ on headphones.
4) Pass sound through a series of TFs - first through HRTFs of 2), then through the inverses of 3), to subtract your imperfect headphones from the chain.