I'm not sure how far that documents the genetic variations in different varieties. I know that we've claimed to sequence "the human genome" without taking swabs from everyone on the planet! My guess is that they have a complete genetic sequence from one variety, and some data on different expressions of some genes.
They did compare "domestic tomato" to a wild cousin Solanum pimpinellifolium and found only 0.6% difference. They found 8% difference between and potato (Solanum tuberosum). For c omparison, humans and chimps are only 1.2% or 2.7% different.
The article claims that the sequence is likely to be used to assist conventional breeding, but not likely to trigger another attempt to market GMO tomatoes like the "FlavrSavr".
It suggested "pest resistance" while using fewer or less pesticides as one goal that will be facilitated. And perhaps "improved flavor" despite the natural non-ripening genes used to extend shelf life.
Also: "because some of the wild species come from desert locations, there are going to be genes we can breed in that will help mitigate climate change."