There is no way for Premiere to export this data separately.
Is there anyway to calculate the cuepoint time, like captionate outputs into an xml file, from SMPTE time values? I can't figure out for the life of me what unit of measurement cuepoint times are... I've been trying to use this guide and it's gathering tools to create XML files with the appropriate cuepoints but I can't figure out the ratio between the cuepoint times vs the SMPTE times... for example I've found this based on video at a framerate of 29.97:
10,000 = 11 sec 26 frames
20,000 = 21 sec 21 frames
30,000 = 31 sec 16 frames
40,000 = 41 sec 11 frames
Clearly the numbers are close, but when I tried to manually double 11:26 it came close, but was a few seconds off from 21:21 (I got 23:22). This discrepency seems too far off to be simply an issue of the framerate technically being a touch more than 29.97.
My brain hurts.
I was looking for an answer to this and came upon a very roundabout solution.
If you have the CS6 or CC suite, you can import your premiere sequence into after effects and use the http://aescripts.com/ft-markerexporter/ script to export xml data. Import the xml into excel or whatever, then divide the time property by 86400 as per http://www.excelforum.com/excel-general/350368-convert-seconds-to-timecode-format.html. you can then reformat the data into HH:MM:SS.000. It's not necessarily frame accurate, but it gets you most of the way.