To make it work I had to choose between something hazardous and something even more hazardous :
1. have the SSD in SATA 1 and a storage disk in SATA5
2. Activate RAID 1 on SATA 5 and reinstall everything.
I choose the fastest way and it seems to work (MDADM is still unhappy but it finally says the raid5 is "clean"). Here's what I did :
I unscrewed the backpanel with sata connectors, I removed the sata 1 and cut some tape to free enough lenght of cable. I pluged the SSD on sata 1.
I plugged the HD storage in the first port, with the cables that used to connect the SSD.
Now the Microserver boots directly on SSD, no usb/SD/raid1 required.
It is an ugly hack which I'm not proud of, but it works.
I guess I'll replace the whole server as soon as I'll have enough money...