Although there are physical differences between the 'blink drive' used in the Dark Matter TV series and 'folding space' in Dune, are the concepts not basically the same?
Not especially, beyond that both are fictional methods of faster-than-light travel.
The Dune series does not focus on the exact mechanics of space travel -- it is not a work of hard science fiction, after all -- but the semi-canonical Dune Encyclopedia gives some tantalizing details. (Note that some of these details conflict with the Brian Herbert sequels, making this answer somewhat specific to the Dune Encyclopedia canon.)
The Spacing Guild implemented space travel using a form of the Holtzman suspensor-nullification effect -- part of the same set of fictional forces that were used to implement defensive shields and suspensors. Activation of the suspensor-nullification effect causes a large sphere ("no more than a kilometer across") to enter "the Void", a sketchily described extradimensional space.
Space travel took place on large spherical ships (presumably sized to fit within the range of the suspensor-nullification effect) called heighliners, under the control of the Spacing Guild. The heighliner is controlled by a group of Guild Navigators. They use the prescience provided by large doses of melange spice to predict and correct for disturbances in the heighliner's course.
I can't find much detailed information on the Dark Matter "blink drive" online, but from what I gather, it's unlike space travel in Dune in several crucial ways:
The "blink drive" is technological in nature. Space travel in Dune requires a biological element (the Guild navigator) to safely complete travel throughout most of the series. (The Dune Encyclopedia mentions that a computerized navigation system was eventually developed, but only in 14132, after the time period of the series.)
The "blink drive" is instantaneous. Space travel in Dune is not instantaneous -- it is faster-than-light, but still takes time.
The "blink drive" can lead to time travel. No such effect is attested anywhere in the Dune series.