i have heard your examples, nice music, thanks for posting.
there is a slight difference between them. actually both sound good, but i would describe the 96k-mix as a little more relaxed in highs/high mids, a little more depth/openness.
I also have a couple of other plugins on the track, including a SonEQ, a Logic compressor, and a Logic Adaptive Limiter, though I don't think those are relevant for the comparison since none of them introduces any SRC.
this is relevant! especially for compressors/limiting.
there is less aliasing when used at 96 k, cause the sidechain-analyzing of the compression/limiting is more exact in the time-domain.
this can affect the sound audibly.
i would expect, that the difference i heard would become even smaller, when you exclude those effects or replace them with nebulas.
would be interesting to hear without these extra vst's.