Your criticism reads like someone accusing economists of being outrageously misleading when they don't sample individual households but measure macro indicators. It's like saying Ramon y cajal was ridiculous because he couldn't image the neuropil effectively. Or like saying early optogenetics experiments were ridiculous because who knows if you're stimulating a neuron in a realistic manner?

And in any case, it's true that synapses are comically small relative to voxel size, but we also have some reasonable information about projection patterns and synapse number from various tracer or rabies studies with which you are no doubt familiar.

I haven't read the nature paper the press release is about and I'm not a huge fan of many d/fMRI practices or derived claims. And I've worked with enough mammalian dwi data to be skeptical of specific connection claims. But this strikes me as a rather interesting result even if you can't measure all the synapses at the right resolution: either the tractography method has connectivity conservation artifacts baked in, or there's something interesting going on.