I can help a little with the root directory: in FAT32 it's just like any other directory or file - a linked list of clusters - except there's a pointer to the first cluster in the BPB. See offset 0x2C at https://en.wikipedia.org/wiki/Design_of_the_FAT_file_system#FAT32_Extended_BIOS_Parameter_Block. FAT32 format utilities generally set this pointer to 2, the first cluster that actually exists on the volume, but strictly speaking, you're right; they don't have to.
The volume label reference I made above is apparently wrong. There was some misleading discussion at reboot.pro that implied Cluster 1 exists: they kept referring to the "first" cluster, which I misread as meaning cluster 1, but actually cluster doesn't exist at all and the "first" cluster they were referring to is cluster 2. I'll edit my last post to fix that mistake.
I think what threw me off was this sentence:
(emphasis added), which I read as referring to an 8-sector "cluster 1" with only the volume name (and a whole lot of wasted space), but now I think it refers to cluster 2, with the volume name and the first several root directory entries.
Anyway, the discussion was whether to put that "first" cluster at the end of a 1 MB page or the start of the next one. The thinking appeared to be: since it only holds the volume label and the first several root directory entries, it wouldn't change often and so shouldn't be placed in the same 1 MB page as the presumably more "dynamic" data clusters that followed it.
But, since 1 MB alignment doesn't seem to matter (at least with the drive I tried) the whole discussion is moot AFAIAC.