The store we bought the suits also mentioned the boots being a weak point. Sooner or later they will leak. He also mentioned that if that happens he can put in some sort of layer which will fix the problem (forever) so I am not too concerned about that. Haven't experienced any problems so far.
I read those comments on Santi's Flexsole boots. Given that most of my drysuit diving is done on the rocky shore of a local lake, I went with the neoprene socks and rock boots option (similar to my DUI suit). It's a bit more of a pain with the extra component, but if the rock boot sole gets worn out, a replacement is much cheaper than replacing the suit boots. I like the design of the Santi rock boots a bit more than the DUI ones because the Santi's use velcro instead of laces which makes them much easier to put on and take off.