WHat if they carve the aon-dor directly on a ship, so it gathers its own power? THe shards create the system of magic, but the magics draws it power from the same source, the universe itself, likly some thing like zero point energy, or energy draw from a vaccume. An elantis ships probally Teleports in jumps, so slowly makes it way through space, making sure its arrival point is clear. Similar to how ships acted in the nBSG. The ships it self would be styled upon the city to ensure they have power.
Scadrial will first need to learn how to imbune their metalic art on to objects, so the ship can increase or decrease it weight or mass, while able to affect the passage of time around it self. So similar to Warp engines or mass effect engines. I am not sure on the numbers but this would mean that the cosmere worlds need to next to each other, or journey will be very far apart.
The map of shadesmar, shows nine locations, it makes me think those nine lacations are the nine other core shard worlds, so either would allow direct travel to that planet, or that worlds version of shadesmar.
THose elantrisians when they entered the pool, did they die, or simply sent some where else. Shard pools are said to be the cognitive aspect of a shard, shadesmar is the cognitive realmm. SHadesmar is said to be the means in which hoid travels the worlds. Is it possible that using the pool simply sent the being beyond the range of the faulty aon dar. Most people believed that the city symbol had stop working, but what if it was faulty instead, actting as a block to the source of energy that fueled them. Aon dars are limited by distance. It may be that the city was built in the form of an aon dar for another purpose than for power, or simply because it was pretty. WOuld explain the refuggees and the world traveling?
I think Roshar could potential be able to create an FTL capable ship, using their skills at magics involving gravity, gravity manipulation could lead to wormholes or teleportation, as well as motion.
THe thing is nalthis is hard to think about in terms of ship creation. ANy ship would have to be a level 4 construct similar to NIghtblood. Awakeninf depends on different factors, breaths, colors, form, commands, so it stands to reason if they make all the other the best and highest, fewer breaths will be needed. What would happen to awakening in a void, would it be able to drain power from the darkness of space of the star light. WHo say its form has to be human, a bird or sea creature could easily travel the stars.