There's a program called Keyboard Maestro that can help with things like this.
You can program keyboard macros to go through and automatically do repetitive things for you. I use it to edit tracks for me based on timecode locations in an excel spreadsheet. For example I can start with a long audio file and some timecode locations, have Keyboard Maestro jump to each location, make a cut and a marker, rename the clip, and move on. At the end it can highlight them all and export them too. It's very fast and fairly consistent (although it does hiccup at times and you have to make sure the macros you created are efficient and clean). You can even program it to move and click the mouse around (and even find the right things to click), there are many possibilities.
And according to this it sounds like if you cut your clips at the points you want markers, it will carry over into the WAV metadata and can be read by some other programs. Use "Export Region Definitions".