Open in Illustrator will create a PDF of the currently open InDesign or Quark file and then attempt to open it up in Adobe Illustrator. By default, OmniMarkz uses the Default Version of Illustrator as seen by your Mac Computer.
If you open a PDF in OmniMarkz, the PDF will simply be passed to Illustrator when you click on Open In Illustrator. The same is true if you open an Illustrator file in OmniMarkz, it will simply be passed to Illustrator when the Open In Illustrator button is pressed.
If you wish to force a PDF to be opened in a specific version of Illustrator, you will need to set up a mini workflow under the Export PDF icon or you could set up a workflow under the Automation Preferences area as well.