Based on the 15 SSR (simple sequence repeat, aka microsatellite) loci they use, the scientists at NCGR in the 2010 Genetica publication do not say that cultivars like VdB and Vista are identical. They call them synonymous. They recognize that their analyses do not prove identity. They picked 15 markers that type (or assort) independently of one another. You can understand that 2 markers near each other on the same chromosome would give you the same information relative to differences and allele frequencies. The 15 SSR loci they use for typing in all likelihood capture all 13 fig chromosomes although I see no direct indication of that. That means that at least 2 pair of markers are on the same chromosome but far enough apart that a high enough rate of crossing over events in those chromosomes cause the markers appear to assort independently. This method of typing is an extremely powerful way to capture major genetic differences as chromosomes evolved different variants which were dispersed when the wasps crossed different fig trees and the seeds generated novel trees. When you look at the detailed typing, what you see is that some loci have a number of versions, called alleles, that are commonly used while others have a couple of common alleles and some very rare ones. The details for those geekish enough to be interested are here:
http://sun.ars-grin.gov/~dbmuqs/cgi-bin/export.pl?action=mrkspread&format=html&cropno=192
So, what could drive the differences between synonymous cultivars that people observe? A number of things occur to me. A highly likely possibility is that the mix of FMD (fig mosaic disease) viruses differs between 2 trees. Their impact on every aspect of the tree from ability to tolerate cold weather to fruit quality is poorly understood. But, when examined, FMD infections negatively impact figs. There are other diseases that attack figs that could result in observed differences. For instance, could the taste difference Jon experienced between Orphan, 278-128 & Deanna be that 278-128 & Deanna were a distance apart from the Orphan tree and both had rust infections that year & Orphan did not? Simple misnaming is always a possibility unfortunately. I have only been playing with figs a couple of years, but I have found it really difficult to trace histories of the cuttings I get. Another possibility is that culturing differences could account for variations people observe. Amount of soil nutrition, water & sun exposure could all drive observed differences between 2 identical trees. Another possibility is something called epigenetic effects. During propagation of higher organisms, a section of a chromosome can get "turned off" resulting in the genes in that area not being expressed. If the genes in that area of the 2 sister chromosomes are identical, then you simply lower the expression level of those genes which can cause observed differences. If there are gene(s) in that area of the 2 sister chromosomes are different and one set is silenced, then there is a distinct possibility of an observable difference or differences.
A big benefit of the genetic tests is that it should allow fig lovers to reduce some of the cultivar confusion out there. Some people get unknowns and call them that. Others get them and apply a new name to what is a common fig for a lot of reasons. The level of discrimination afforded by SSRs allow you to say how closely related 2 different fig cultivars are and to group different cultivars into families. The information in the Genetica paper allows me to try to collect figs from different families and ones that help define the range of differences. It also allows me to try to get similar versions of the highest rated figs to try side-by-side. For instance, I want to collect Sucrette, Black Madeira & Gazir for the fun of it (2/3s of the way there). While I do pay attention to differences people note between synonymous cultivars, I decided to not collect them. So, based on Jon's opinion that his Vista performs better for him than his VdB, I got a Vista from him last year and will not get a VdB. No doubt, many will think I am missing out. But that is some of the fun of it.
Good luck with your figs!