Hi Bryan,
I am also integrating Mender on a Zynq 7000 series board using Petalinux 2018.3.
To balance what you said, there are some Xilinx wiki pages on how to work with pure Yocto. Plus I did not have particular problems using rocko version of Yocto.
However, I agree on using Petalinux being the main challenge : I have been struggling (and still am) with Petalinux scripts which are not open-source and perform obscure and awkward Yocto files generation…
I think having a Xilinx Zynq board integration could be nice, but I am afraid it should not use Petalinux tools, because it seem to require a lot of work - sometimes only just trying to bypass petalinux logic. Also it does not seem stable enough, they regularly change a lot of stuff between versions.
Concerning FIT images:
Maybe this is not what you want, but I managed to disable FIT image generation to use a zImage instead (compatible with mender), ask me if you need help for that !
Nicolas