It actually just causes CoreAnimation fence issues and messy animations as far as I can tell, but you're entirely right. Fixing in my next commit (which also fixes some other brokenness). Even had a note in the TODO about it.
This is the first time I've used MobileSubstrate and Logos, so I'm having a lot of fun :)
You may only be seeing CoreAnimation fencing issues, but the fact is, you're accessing main-thread-only classes from a background thread, and it has the potential to corrupt data structures which can lead to crashes and other bad behavior.
This is the first time I've used MobileSubstrate and Logos, so I'm having a lot of fun :)
update: fixed.