The 2 GB limit is irrelevant of file system. dd doesn't know about or
care about file systems. So creating another partition with another file
system would have no affect on dd. Block size is not the same as
volume/partition size. The volume size is the block size times the
number of blocks. Having very large block sizes is a bad idea for a
persistent drive. There is a reason dd doesn't allow block sizes larger
than 2 GB, we shouldn't try to get around that.

There is a simple patch in the bug report I linked to that will change
it to use 1KB block size. Usb-creator would work correctly with that
patch and the persistent drive would be created faster and it would work
better for its intended purpose. I think creating a 2nd partition on the
drive introduces a lot more complexity and gives little benefit.
Remember the persistence file isn't for your data. You can store that in
a folder on the regual vfat partition. The persistence file is just for
changes in settings, software updates, etc. Four GB should be plenty for
the vast majority of users. Also being able to access data on multiple
operating systems is often important for flash drive users. A 2nd
partition will not be accessible in windows regardless of file system.

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calling dd with block size > 2GB causes casper-rw not to be created
https://bugs.launchpad.net/bugs/352766
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