Hi Martin,
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As an example it will not make any sense to run a tool that demonstrates the use of a RS-232 IP on an FPGA on an ARM processor (whose RS-232 is completely different from Altera's one) and vice versa.
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You've missed a critical piece of information; the Cortex-M1 is a soft-core ARM (Arrow supplies the IP).
An SOPC or Qsys system can be created with an ARM Cortex-M1 Avalon-MM master, and an Altera Avalon-MM slave UART, and hence the UART would be identical to that used for a Nios II processor.
I'm not sure that the Cortex-M1 gained much traction though. I haven't seen many people asking questions about its use on this forum.
Cheers,
Dave