Show text in a video at certain time in the video

The cue points are still based on the slide timeline right?

Yes

If the video is paused, the slide timeline still goes on, which means the cue points are not accurate or related to the video.

No

While there really is no way to keep track of where a video is if you let the user drag its timeline, you can control it. It all hinges on starting the video when the slide starts and not showing the Video timeline. Then the two of them cannot get out of synch.

If you want to let them pause it, use the "Pause timeline on this slide when user clicks ..." and "Resume the timeline on this slide when user clicks ..."
That will allow the user to pause it, and your timing will be correct.

Dragging the slide scrollbar around is going to work only if the video starts with the slide and uses the slide timeline. Then the slide timeline can be used instead of the video timeline. Allowing the user to drag the seekhead around comes with other problems, so I prefer to use the pause, but you may have your own way of doing things.