If you want to get the extracted gamut referenced view to look better, you could profile the projector without having adjusted D65. That should give you a more or less flat RGB balance. It won't be totally flat because the gamma of your projector panels I think will be slightly different between the 3 channels, which when you think about it causes colours to vary from where they should be, as it means the rate they go from 0% output to 100% output is different. It's like mixing paint(ish).
There are arguments for and against adjusting the PJ to D65 in its menus using the RGB gains. In an ideal world you probably wouldn't use any display controls, and just leave all adjustment to the 3D LUT. However, in the real world, a lot of LUT holders are only video legal levels 16-235 (I know my Lumagen is in this camp). What this means is their last control point is at 235,235,235, so you can control the top corner of video white if you imagine a colour cube. If your content does have any values above 235 in it (can be from encoding issues, colour conversion in players, specifically crafted test content, etc) then because 255,255,255 doesn't have any LUT control, what you'll have is perfect white up to 235, an from 235 to 255 the whites will change colour towards the native white point of the projector. If you look at a whites (contrast) test pattern from something like Ted's disk, the visual effect you'll get is that you have a colour shift in your white at the top end.
I'm not sure the custom filters are enabled in Colourspace yet - at least I don't think I could work out how to get them up. I opened up the profile in Lightspace to view, which isn't as nice as you can't zoom into the corner of the CIE chart to fully see the stacking of the points.
I do understand why you want to try and get that workflow to work better; I've discussed with Steve a couple times and it would be nice if the SW would deal with this kind of display profile a bit better automagically. To be honest I think the concatenation etc features themselves works perfectly fine for what it is -general purpose LUT manipulations designed for colour professionals (which I am not, I'm just a bit further down the calibration rabbit-hole than you
!). It is the application of the feature to this issue of these profiles that can be hit or miss, as I don't think many folk understand it enough to realise it only works once you get rid of all those duplicates appearing in the profile, which needs a quite reduced intermediate gamut for some displays.
I can't honestly remember the exact detail of which order the concatenation works with... I did work it out once but has since been forgotten as I don't use it anymore past originally working out that the gamut needed reducing a lot! If you want to try and work it out easier during your test, maybe use an obviously different gamut as the intermediate instead of one that is very close in size to the display native (it will make it easier for you to understand how it works).
If you are interested to play with other aspects of the SW - there is another approach to this also outside of LUT concatenation, which is to doctor the patch set used; so you can pre-treat the patch set with a suitably smaller sub-gamut to remove the patch areas that are problematic from the profile, export the patch list, and then just add back to the patch list manually the far extents of the colour cube (so probably the primaries and secondaries, ie (255,0,0) , (0,255,0) , (0,0,255) etc. At the time I was investigating I actually thought this worked better.
A well-mannered display should have a non-colour managed mode for when you want to do 3DLUT, which is what the Profile off mode is in the JVC. Unfortunately up until now, JVC have not implemented a Profile off mode with the cinema filter in. They're just about to release an update to the current consumer series N5-NX9 that finally enables this option (yay!). Without it you have to jump through a hoop to force the filter in with a "diagnostic" IP command. I know that with the built in colour profiles the filter causes way too much loss of light for a lot of folk; it would be interesting to know if you use profile off and force the filter in with the IP command exactly how much light is lost. It might not be anywhere near as lossy in Profile off with a 3DLUT externally than in the built in modes.
You previously asked about damage to your PJ - I think it is unlikely. I've never seen any hint of image retention or similar on my X7900. I'd still never leave a single patch on screen for hours on end though, that's just asking for trouble. In terms of your drift graph - I see a few possibilities. Either there is some drifting response of the panels to the level of the image displayed, or there is an inherent instability in the JVC projector (maybe it always cycles the fans from slow to fast to keep the laser just right, which causes the waves) or maybe the environment the PJ is in causes it to have to cycle the fans more aggressively.
OLED TVs behave in the first way. The patch sequences in Lightspace and Colourspace aren't perfectly balanced in terms of the luminance throughout the sequence; it used to be quite bad (there are some posts on here somewhere) and now they're very good, but there are still some better results for drift that can be had with a specialist patch set. I did some work a while back to try and help friends with OLED TVs which culminated in a patch sequence sorter that more or less eliminated their drift patterns.
You might try some of the patch sets attached. These have been sorted with an algorithm to try and balance for WRGB pixel displays, but I think it should also work for RGB pixel displays. The patch sets are interesting in that they also have a larger set of values in the greyscale, primaries and secondaries, which can sometimes be useful. It will be interesting to see if you still get that characteristic drift with these sets. For each size there are two sets; one is a pre-roll set which is used for getting a panel up to temperature, and the other is a full patch set.
Have fun anyway.