[INFO] Transformer Boot Flow
I figured I'd illustrate the basic boot process flow for the Transformer. This should help conceptualize what the Transformer does when running stock Android, custom ROM with CWM Recovery, or something even more custom, like dual-booting Ubuntu. I'll add onto this as I have time and learn more.
Boot Modes
Normal Boot - By default the Transformer will boot up and load the Android boot configuration from the boot partition, which ultimately loads the OS from the System partition. Once Android loads, you'll see these partitions mounted to /boot and /system.
Recovery - When you boot the Transformer by holding Power+VolDown and then press VolUp when prompted, the Recovery partition is loaded. I don't actually know what the stock recovery looks like, since I rooted almost immediately, but this is where the ClockWorkMod (CWM) Recovery is installed. While I left this out of the diagram, this partition should have write access to most of the internal flash.
APX Mode - When you boot the Transformer by holding Power+VolUp, APX mode is started. This is a bit different from the other two boot modes, as the internal flash isn't used. Instead the APX Mode is booted from another read-only chip, which has direct write-access to the entire internal flash. This is the mode that nvflash communicates with to backup from or write to the flash. If your Transformer is nvflash-able, you should also be un-brickable because of this mode.
Partitions
Boot - This partition stored the boot configuration for Android. As with any Linux-based operating system, this partition is necessary to start the OS. Eventually the remaining OS files are loaded from the System partition.
System - This is where most of the Android OS files are located. Generally this partition is mounted as read-only, as removing or editing the wrong file could bork your Android installation.
Recovery - This partition stores the recovery software, such as the stock recovery or ClockWorkMod (CWM) Recovery.
Data - This partition is used for application and user data storage. This is generally the largest partition, so some custom configurations (such as dual-boot Ubuntu) will shrink this partition to steal some extra space for their own use.
Cache - This partition is used for Android cache. As I don't know much about how Android uses this partition, I don't have a better explanation.
Notes:- Please reply with any requests or fixes. This is a Work-In-Progress.