I just verified it with a new apitrace. There is indeed glFenceSync() being
called. Frame 3 now looks like:

1510 @0 glFenceSync(condition = GL_SYNC_GPU_COMMANDS_COMPLETE, flags = 0) =
0x8c47bf0
1511 @0 glFlush()
1512 @0 glClientWaitSync(sync = 0x8c47bf0, flags = GL_SYNC_FLUSH_COMMANDS_BIT,
timeout = 0) = GL_TIMEOUT_EXPIRED
1513 @0 glClientWaitSync(sync = 0x8c47bf0, flags = 0x0, timeout = 0) =
GL_ALREADY_SIGNALED
1514 @0 glBegin(mode = GL_QUADS)
1515 @0 glTexCoord2d(s = 0, t = nan)
...
1523 @0 glEnd()
1524 @0 glXSwapBuffers(dpy = 0x88db6a0, drawable = 83886088)

and onto Frame 4, and so forth.