I don't think this is correct at all - are you sure that all three samples have R=0.25, G=0.25, B=0.25, but A=0.5? I don't see this and would be surprised if that was the case. I see this from DeepSample_DCX (see the attached screenshots as well):
5 {1.0 1.0 0.25 0.25 0.25 0.25} partial,additive
4 {1.0 1.0 0.25 0.25 0.25 0.25} partial,additive
3 {1.0 1.0 0.5 0.5 0.5 0.5 } full
2 {0.9 0.9 0.25 0.25 0.25 0.25} partial,additive
1 {0.9 0.9 0.25 0.25 0.25 0.25} partial,additive
0 {0.9 0.9 0.5 0.5 0.5 0.5 } full
If you can verify against the screenshots your sample values and please respond with screenshots of your own, if you are seeing those anomalous values then something is wrong.
You may already know this from our previous correspondence but I'll go over it again, I'm still in the process of writing this part of the docs up:
This is where the new 2.2.2 partial subpixel-coverage encoding comes into play. You should open the DeepSubpixelMask node in that script and change the 'do sample' knob to see each sample's metadata values.
At certain fractional subpixel offsets the 8x8 spmask abuffer doesn't have enough resolution to adequately capture the coverage weight, leading to aliasing of the transformed image. Increasing the spmask resolution is not a practical option so to compensate I expanded the partial-spcoverage flag from a single bit to 9bits (only 8 bits are actually stored since 0x00 is logically the same as 0x100, so the 9th bit is implied) which gives 0-256 levels of partial subpixel-coverage weight.
A sample who's transformed subpixel bins straddle multiple output subpixel bins is split into multiple output deep samples, where one output sample has the full-spcoverage mask with no value weighting and the other output samples are the partial-spcoverage samples that include value weighting and are additive. Additive-ness is a key detail when flattening these samples!
So, if DeepSubpixelMask is looking at pixel 512,93 in the test script and you're looking at sample 0 you should see metadata 'flags [none(Log,NoMatte]' and an spmask pattern that's missing column 5. Sample 1 has metadata 'flags [Log,Additive,spCvg(0.500)]' with a spmask pattern that fills in column 5. Continue down the sample list and you'll see the alternating pattern of full/partial spmasks.
The reason that samples 1,2 and 4,5 are duplicates is that the combiner method failed to combine those samples together into a 0.5 full-spcoverage sample. The combiner can be improved in this respect as there are cases where the output does not flatten to exactly the right answer - try transforming by x500.7 y0.3 which outputs 0.74609 instead of 0.75.