I have an MTX explorer rack and one of the medium trunk bags with fold out "panniers". They are great and the trunk bag was my first commuting bag but I graduated to true panniers fairly quickly and never looked back.

The pannier (usually just one) keeps the weight lower and seem more usable and versatile. I'm sure some of it is also because the true panniers look a bit more "real" and classic in my mind. It hasn't crossed my mind to break out the Topeak bag in a long time.