I actually don't think the X-sync thing is a problem, depending on what impulses you're lining up the time measurements with. There are four events:
1) first curtain travel starts
2) second curtain travel starts
3) first curtain travel completes
4) second curtain travel completes
Slower than X-sync, the ordering is 1, 3, 2, 4 and faster than X-sync, it's 1, 2, 3, 4. As long as you measure the timing offset between 1 and 2 or between 3 and 4, that's the shutter time. The travel time (1-3 and 2-4) is irrelevant to the exposure.
The above assumes that it's possible to make out these four distinct events of course, and that may not be possible depending on the shutter design. And it assumes that the user knows enough to select the correct pair of events, the ordering of which depends on the relationship between shutter speed and x-sync.