Thanks for the replies. Some responses;
Concerning the current flatfield algorithm: speckled whites in custom targets to start with, but is already possible to use with ColorChecker Digital SG. Regardless what Rawdigger folks is thinking I think it's a better method than switching in a gray card, as you only get one shot and can thus use it in changing outdoor light. Looking at the difference it makes from a typical well-exposed shot in outdoor overcast light I'd say that it doesn't make much of a real difference, corrections are around 3-4% or so, you won't really see a difference in the resulting profile. I haven't tried to push it with really uneven light though.
Flatfield correction with a white plexi I'm very familiar with as I shoot with a MFD tech cam (they have color cast issues on wide angle lenses), I don't think that will contribute any additional value than the flatfield on speckled whites as I do now.
The thing is that I'm seeing unexplained issues in some test charts I'm doing, which seems that the camera is registering too low saturation of the colors. When I do a simulation with the same target using the camera's spectral sensitivity functions it works out fine, so I'm thinking that I could have some issues with contrast. Flare sounds like a theory, but I don't know how to model that, simple linear reduction of contrast, measured on black vs white patches? If flare is badly non-linear so it really can't be modeled we'll have to live with it.
I've attached how the test shot looks (not too flare-prone shooting condition, right?), here a linear rendering with the SSF-generated profile applied (which makes up a correct result). The test chart is simply printed on semigloss paper using a pigment inkjet, spectral spread is not super-good but not too bad either. I'm investigating the performance of these custom charts. In simulations they do fine as said, but I get problems in practice. I'll test make a matte chart and see if it works better with less saturated colors too. (The chart has only maximally saturated light colors, ie no brown as it's just dark orange, which is also a test I'm doing, as the LUT is 2.5D dark patches should really not be needed.) And yes, the paper is OBA-free.
Most likely a lower saturation target will work better, it seems like high saturation colors makes errors worse, and well it's quite natural as with higher saturation colors you have the less linear combinations of the camera raw channels will work. I do not yet know however if high saturation color patches on a target is impossible due to measurement limitations, or if they can be made to work. Of course there's also a risk that I've made some bug, but I don't think so as the profiling works fine if I feed it with the same target spectra and the camera's SSF.