The percentage of bonus xp that you gain from using a story point is a percentage of the xp cost of a point. So at max level, where each level is 4 million xp and you get a total of 4 story points over that period, the % is of 1 million bonus xp. So an action that gives 50% bonus xp will give you 500k, and one that gives 100% will give you an even million.
It can be seen as a long run discount on the story point expenditure, since if you start with 0 bonus xp and zero progress towards the next point, and spend a story point with 100% bonus xp, then, when you have gained 1 million base xp, all of your bonus xp will be gone and you will have two story points, where you otherwise would have just one. The higher the bonus xp, the "cheaper" the story point cost is, when all is said and done.
The only quibble I have with the current system is that it isn't too hard to run a bonus xp surplus. If you spend story points with on average over 50% bonus xp, you won't actually ever run out of bonus xp, as you gain a new story point before actually running out of the bonus xp from the last one, and so your bonus xp total can grow and grow, and those higher bonus xp values end up not really meaning anything, since you never really collect all the bonus xp. Admittedly though this does discourage spamming the "get out of a jam free card" story point uses, since over using them compared to things like capital ship build ins and colony improvements eventually makes them cost more in a sense, which may be a good thing in the end.
What I would love though is more opportunities to spend story points on finding blueprints and pointers to other shiny exploration things. My current game has gotten to the point where there isn't much of interest left, so finding anything new is really difficult, and I'd love to be able to pay to get pointed in the right direction more frequently.