I've been trying daily builds for years now hoping for some improvement with this issue but no dice.
If you've not seen _any_ change then you've not been trying daily builds "for years."
(Because if you had, you'd have definitely noticed better battery life, combined with massive drive corruption. Take your pick.)
What I don't understand is why the stock firmware has no such problems. What does the stock firmware know that Rockbox doesn't?
The Apple firmware doesn't (1) ever completely power the iPod off, and (2) perform writes when you're not performing iTunes synchronizations.
The bottom line is that those ATA<->SD adapters don't support the *mandatory* ATA commands that ensure all writes are safely flushed (ie "safe to shut down") and _also_ fail to recover properly if you issue the shutdown command they they (illegally) don't claim to support. Compounding this, many (most?) SD cards are quite power hungry even when completely idle, so if we can't power them down, we're going to end up burning more power than even the old spinning rust uses.