I was just happily surprised. It's been a while since we've had posts from you
What is who afraid of? The answer is almost certainly spoilers, yes, but I'm not sure if you mean the Shiplords or the Uninvolved.
It has been a while. Too long, really.
The Shiplords. Everything I see about them says that something Really Bad™ happened long ago and they are not only willing to die to prevent it from happening again, but to inflict horrors on innocents that they seem to want to help. Their claim of being 'friends' combined with the statement that looking to their origins prevented a war says that there is something powerful motivating them. Either they are trying to protect the younger races from an external threat, from each other, or somehow from themselves. The only other possibility that comes to mind is if they are actively trying to push other races towards ascension, but that may just be the best solution they've come up with to whatever other problem they are trying to solve.
So the possibilities I see are this:
1) There is something hostile lurking in the void. If it was simply a military threat then the Shiplords have had plenty of time to build up, so it isn't something they can effectively fight directly. Do Not Linger and minimum FTL standards support this.
2) Left unsupervised the galaxy tends towards continuous warfare. Weaker races tend to get overrun easily and stronger ones tend to overwhelm their neighbours. Wiping out both extremes tends to keep things balanced, limiting the total carnage, and continual poking encourages those that remain to focus on defence instead of attacking their neighbours.
3) Naive use of certain secrets can easily get out of control, resulting in galaxy-wide threats. The restrictions on bio-modification and AI research fit this pattern.
4) The Shiplords regard ascension as a noble thing, but are unable to do it themselves. Whether this is due to actual inability or an unwillingness to leave anyone behind remains to be seen, but they are trying to help and encourage others to do it. Also the end goal, is it nihilism (end of suffering) or do they believe that there is a higher existence that is preferable (everybody (but them) goes to heaven)? Or just a general failure on their part to understand what the Uninvolved really are, mistaking them for a better state of being?
So 1) would be Space Cthulhu, 2) and 3) Mass Effect, and 4) a less cynical Uplift Wars.
The fun part is that none of these are exclusive with any of the others.