Nopes. Cannot ignore the error.
If you actually ignore, there will be two sections with the same name, one with the "memory" attribute and the other without.
If you just add a memory region on top of the memory section, you wont be able to put any linker section on it because the pulldown boxes will not have it.
If you add a new memory device with another name, HAL even compiles OK but the actual project fails in compilation time with a crazy offset error out of boundaries.
I finally got it done by adding the "isDeviceMemory" to "1" in the module "mm_bridge", interface "s0" in the nios.socpinfo file. It is a PITA to find the right location. XML is unreadable.
I'm sure this will get reset next time I regenerate the HDL files.
Wonder if there is any other way. Wish there was a button in GUI somewhere to make this easier.