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.
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.