I have this similar quest some time ago and did alot of research on it, in the end i was able to make it work perfectly but under the following conditions only.
- Both the RouterOS and the interface hotspot are the same machine.
- I have to downgrade to v3.5, any thing higher than that, it does not work, infact Mikrotik say it will not work but I believe it should works, so i kept on trying with older version where you can ping other local loop ip other than 127.0.0.1 ie you can reach 127.0.0.2 … from the routeros.
How I did it, if you are interested may be you can continue from there!
setup diffrent hotspot on different interfaces (NIC) on the router,
configure them with normal radius configuration, on each you use a diffrent loop address say 127.0.0.1, 127.0.0.2, etc also specify diffrent domain say domain1, domain2, etc accordingly, then you configure thier respective customer in the usermanger.
This done cafrefully work perfect. I have removed the configuration otherwise, i would have paste the configuration live but can still see the configuration virtually.
Need further details, halla back but be specific.
View similar topic on the forum here: http://forum.mikrotik.com/t/running-two-hotspot-on-diff-interface-in-a-single-router-os/36416/1