Unfortunately my TX1 won’t arrive until next week, so I have no way to look at what defaults will do. Default should probably not reuse system.img, the “-r” option should be required for reuse unless there is some paradigm change in how the flash should behave by default.
In particular, if the “-r” option (listed as causing reuse of system.img) causes use of system.img, then we would suddenly need a new option to “not” reuse system.img…and I do not see such an option. Anything else which is being reused probably does not matter…but I would still wonder about this since modifying a “reused” system.img under u-boot would seem like a “no no”. For files which might be used under another bootloader (especially fastboot), many of those files being reused would instead go into other partitions without modifying system.img, so their reuse would be irrelevant to preserving an existing system.img. Perhaps the message of reusing system.img is just bad and system.img wasn’t really reused?
What was your exact command line for the flash? The fact that USB in recovery enumerates is encouraging, but I’m also wondering if there is a glitch in the flash program (or the command line used for this flash).