All right, maybe you could try if that ppa facility can build your modified source package into one that is installable with a ppa sources.list entry. I think mdadm --incremental needs the map file in the system to be successfull with later hot-plugging of raid devices. At least what I remember from when I last tried is that hot-plugging worked in initramfs, but not in the running system. I don't know, maybe initramfs already does some copying of /var/run and it will just work if you enable mdadm to create the mapfile there and it can can also find it there later.
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