If you don't mind me asking: if the goal is embedded systems, why use FAT at all? I think that this relates back to Brendan's point, as his whole argument was that much of the trouble came from using FAT32 in the first place.
I am not saying that you shouldn't use FAT (though I personally don't recommend it), but it might help if you could explain why you chose FAT over, say, SFS or ext2.
For that matter, just what sort of 'embedded applications' are you aiming at? I gather that this is still going to be on the standard PC platform (otherwise the whole issue would be different - even if the platform still uses an x86 CPU, an industrial controller or an SBC such as an UDOO X86 wouldn't necessarily be all that similar to a PC in other regards) which implies that it is a control unit for some remote device rather than as a microcontroller type unit. You'd be looking at similar use cases to, say, RDOS, or Qnx, or Menuet, rather than, say, most eCos installations.
So, some additional information about your desired results might help here.
EDIT: Looking back over your previous posts (including some I had responded to myself, including
one where I had previously mentioned SFS) I see that in the past you have argued that you needed FAT support in order to support data cards and Flash memory drives. However, needing to
support FAT32 doesn't imply needing to
boot from a FAT32 disk.
It
is possible to format (for example) a microSD card in a different file system (or even some ad-hoc partition structure with just your OS in it), and boot from that, while still being able to read and write to FAT32 partitions (even on the same device - yes, such devices can be partitioned, though some older models of Flash drives require you to respect a hidden partition containing proprietary code, something that would usually preclude their use on anything other than a Windows PC anyway).
This might be particularly relevant regarding an embedded controller or SBC, though admittedly some such devices have their own limitations in this regard (e.g., the weird boot structure used by the RPi).