If you just want to vary parameters for a baseline geometry, the I suggest you use the 'Design Variable' functionality. It allows you to choose which variables to vary and provides an easy way to 'apply' those changes to your baseline file. You can then use a simple *.vspscript to automate whatever analysis/export you need from OpenVSP.
The same functionality can be used with *.DES files or *.XDDM files -- the latter is an XML format defined by the Cart3D optimization framework -- i.e. OpenVSP is a drop-in geometry engine for Cart3D shape optimization.
If you need more sophisticated 'driving' of OpenVSP from Matlab, there are a couple of ways you might proceed. This is the way to go if you need to generate models from scratch (no baseline files), or perform more complex use of the OpenVSP API.
It should be possible to call OpenVSP directly from Matlab in two ways. You will need to be able to compile OpenVSP yourself -- and you'll need to be a bit of a hacker.... SWIG is a wrapper interface generator that OpenVSP uses to create the Python wrapper. It can also generate Java wrappers and in recent development versions, Matlab wrappers. Matlab can call the Java wrappers if need be -- or perhaps the development Matlab version could be made to work.
However, I suggest you try just using the *.des file and see how far you can get.
Rob