Hi Patrice,
OK. Please, verify first that you can boot µClinux without Xenomai on your board with the 2 extra hrtimer and hrclock peripherals.
There is no priority on IRQ with NIOS.

So, If I have understood, I could put:
IRO = 7 for hrtimer
IRQ = 8 for hrclock
IRQ = 1 for sys_clk_timer
with  this configuration µClinux without Xenomai with the 2 extra hrtimer and hrclock peripherals can boot  on the board .
But I'm wondering why with the first configuration (IRO = 1 for hrtimer,IRQ = 2 for hrclock and IRQ = 3 for sys_clk_timer), it didn't boot?
Please verify that you have correctly enabled all the right options under SOPC builder for hrtimer and hrclock.
Because we have flexibility in HW configuration with SoPC, we must be more careful.

Configuration of hrtimer with the SoPC Builder:
• Timer: 32 bits.
• Timeout period: 1 µs.
• Preset : custom. Writable period, readable snapshot, Start/Stop control bits.

Configuration of hrclock with the SoPC Builder:
in the snapshot mode. Its configuration with the SoPC Builder tool is:
• 64-bit timer.
• Timeout period: 5 clocks. clock=20 ns (100 ns). The timer functionality is not used by Xenomai.
• Preset: custom. Writable period, readable snapshot, Start/Stop control bits.

Is it correct?
According to errno.h, code -19  is ENODEV, please verify your timer configuration and respect naming convention
Here, you speek about "sys_clock_timer"?
Configuration of sys_clock_timer with the SoPC Builder:
• 32-bit timer.
• Timeout period: 10 ms.
• Preset: custom. Writable period, readable snapshot, Start/Stop control bits.

Regards,