Its a very cool origin conceptually but it has a few issues, the most glaring one I've seen is that if your Ark is forced to go missing in action (e.g. stumbling on to fallen empire territory) it has to go all the way back to your starting system and that can take many years of you just having to sit and wait.
One solution could be to have the Ark accompanied by some regular science ships or "probe" ships, giving it a higher sensor level or if possible my preferred option of giving it a massive "missing in action" time reduction.