WK,
I couldn't get access to the whole paper, but I had a few questions that you might have been able to glean.
This previously undescribed process is shown to occur at all DNA sequence polymorphisms examined...
1. So, not just their pet gene?
2. Did they arrive at this homozygous recessive gene through crossing (well, I guess so since transposons typically land in more than one place as I recall)?
3. Is it possible it "mutated" back to the original sequence?
Besides I agree with you in that I certainly don't think one gene in any way confounds the ToE.
Lastly, the paper you cited was a polyploid plant...maybe I'm too new to the whole science arena, but I didn't find that particularly surprising.