My speculation on why the Nikon D800E does not simply omit the two (somewhat expensive) layers that make up the OLPF is that
- this would slightly change the optical path and thus where precise focus occurs, but
- this change would not affect the optical path to the PD AF sensors or the OVF,
so there would be a discrepancy, leading to slight focusing errors with both AF and MF. To correct that could require a slight mechanical change to the mirror/focusing/VF assembly, and having two versions of that assembly (one for cameras with anti-aliasing, one for cameras with aliasing) would have cost more.
I believe this is precisely the reason Nikon took this path with the OLP filter implementation (pun intended post writing). Thirty years in high-tech manufacturing has taught me that itís all about production costs and (hopefully) continuous improvement, providing a better product with each generation, while lowering production costs and price to the end user.
I agree that the effective light path must be made effectively same for both cameras to maintain consistency and commonality in the production line and avoid mechanical differences or adjustments between the two cameras. However, this might also be accomplished by using appropriate thicknesses of less expensive optical glass plates in the D800E to replace the crossed birefringent elements in the D800 (similar to what companies like LifePixel do when they remove the OLPF).
But there is one possibility I havenít seen in this discussion that may explain Nikonís choice to re-use the D800 birefringent filter(s) on the D800E. A while back I read a technical white paper on trends in manufacturing of digital camera sensors. It wasnít specific to Nikon, but did mention Sony. With the goal of simplifying the manufacture of both sensors and cameras, the optical components in the filter stack on the sensors are being reduced. One of those components is the optical glass cover normally installed on the sensor package during sensor fab. (presumably done by Sony for the D800/E cameras).
The clear sensor filter is being replaced with one of the two birefringent filters, making it integral with the CMOS sensor package (and not economically feasible to remove). If this is the case with the sensor Sony delivers to Nikon for the D800/E (and I think this highly likely), it would explain Nikonís approach of simply rotating that second birefringent filter (along with the necessity of replacing the integral wave plate/IR filter set between the two birefringent filters to eliminate the un-need wave plate). So I think Nikonís published diagram of the D800/E filter stack is essentially correct: http://www.nikonusa.com/en_US/IMG/Images/Learn-And-Explore/2012/Camera-Technology/D-SLR-Series/Moire-D800-D800E/Media/OLPF_schematic.pdf
Except that it doesnít show if the one of the birefringent plates is permanently installed on the sensor.
The cost savings here are obvious---Sony supply one identical part to Nikon for both cameras simplifying their sensor fab. line. And Nikon only has to change their line toward the end when the filter stack is installed to determine if the camera will be a D800 or D800E. Also, the reduction in components and air-glass interfaces should result in both lower production costs and higher final image quality. The savings should more than offset the possible extra cost of the birefringent filters in the D800E. A company like LifePixel could confirm if this is indeed the case for the D800 and other newer cameras. It will make a bit more difficult for them when converting such a camera to remove the OLPF. Their only choice when converting a D800 to eliminate the OLPF effect may be to do what Nikon does.
For future possibilities, thereís been a lot of progress over the past few years on the development of electrically-tunable birefringent filters. They are already being successfully used in high-end space and military imaging applications. The current costs to implement these in a high-volume consumer cameras may still be prohibitive. But I wouldnít be surprised to see these in future digital cameras. Imagine having a dial or menu item where you can select a variable range of OLP filter effect from say 0 to 10, that you can set according to the subject!
And taking this concept further, since most tunable birefringent filters are based on LCD technology, with clear thin-film electrodes applied to the active LCD plates, there is no reason that the conductive layer couldnít be patterned into a grid that would match the sensel grid (or the Bayer pattern). If placed directly over the sensel grid, the OLPF effect could be controlled for each individual sensel (or RGB group in the Bayer filter). If combined with an in-camera image processor smart enough to detect aliasing and moirť in the scene, it could dynamically, locally resolve any aliasing issues during capture for the affected areas of the image, while leaving the unaffected parts of the scene alone.
And Iíll offer one more trip into current science fiction land, based on the same concepts. It is also possible to construct electrically-tunable neutral density filters using LCD technology. Place such an ND filter grid over the sensor and it could be possible to individually control the sensitivity of each sensel. If combined with something like Tony Kuyperís PS luminosity masks (but implemented in the cameraís image processor), the sensor response might be locally tuned to dramatically increase dynamic range during capture---operating as an adaptable, super-GND filter automatically reducing exposure in highlight areas.