I may have to break one of the 3 rules of magic, sorta. And not the ones about creating/destroying matter, or bringing things back to life. I was planning on using semi teleportation. Its not exactly instant, and it is definitely not without error or risk. think of time as a part of a co-ordinate set, once you leave your origin you are kinda throwing a dart in 6 dimensions and trying to arrive at the right place/time/state of being. (you can arrive dead)
Edit for post script:
Idea, sail the ship through the metaplanes.
Edit for post script:
Idea, sail the ship through the metaplanes.
Problem with sending anything through the metaplanes is that you can't really take physical forms with you and if you exit in a mana void you're pretty likely to just explode.
What you might be able to do is take the possessed world tree idea and expand it to more of a grove. Have the tree-hugger space-faring mages be an inhabitation tradition and inhabit each tree in the grove with a plant spirit that can use the Movement power. House rule something allowing the Body restriction of Movement to be circumvented by having a group of spirits all using the power at once on the same heavy object, something like the combined force of each spirit being used to determine the max body of the target able to be affected by the power. Considering that the max speed record of a space shuttle on re-entry was 8000 m/s and that 270+ years in the future at shadowrun technological development levels will put us at something significantly higher than that, then multiplying by around 6 for magic and you'll have a ship pushing the speed of light, or even exceeding it if you're being generous and saying fuck you to physics in favor of magic. You still won't be able to travel the stars in anything like a hurry but you'll be able to at least have a chance of making it to Alpha Centauri before having all your passengers die of old age.
As for the human feces as fertilizer idea, I suggested it as a way of creating a circulating, natural system on board the ship reminiscent of Earth, which should create a more powerful manasphere. And if the people providing the fertilizer are all being fed by the regenerating magic trees at the center of the ship then it won't be corrupted industrialized poo, it'll be magic poo. So the secret to interstellar travel is magic poo