Imagine this scenario: In order to get DTmin to 0 you must do a retrograde burn but this burn dips your orbit into the atmosphere. What do you do?
I remember running into this problem when I was first learning to rendezvous. In my case, the problem was that the object I was trying to rendezvous with (the ISS) was pretty much on the other side of the planet. Even when I set Sync Orbit to display 18 orbits I found that I still needed such a large change to my DTmin that it wasn't workable. (See image below)
What I eventually came to realize was that I should simply use time warp to close the distance between my vessel and the ISS - with no regard to Sync Orbit MFD
until I was within at least 1/4 of an orbit from the target. (See image below)
Once you are within a 1/4 of an orbit from the target, you should be able to use Sync Orbit MFD without having to worry about dipping into the atmosphere. Also keep in mind that the closer your orbit matches your target, the closer you can get before having to set up Sync Orbit MFD. In these image examples, my ship's total time for one orbit (T) is 5,433 seconds. My target's T is 5,501 seconds, so our orbits are pretty closely matched already. This means I can get quite a bit closer to the target before setting up Sync Orbit MFD. (See last image below.)