Hello Ramon,
Sorry for such a delayed reply.
As per the "iw" documentation depending on the driver we should be able to create multiple wireless interfaces on a single wireless card and connect them to different networks.

I also checked on my VM where I am running mininet-wifi using "iw phy" there are 2048 of interface combinations that seem to be supported.
If I am not understanding these wrongly, we should be able to create multiple mesh SSID links between two AP's.
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I created a scenario where there are 4 AP's (ap1,ap2,ap3,ap4). AP1 and AP2 will have 4 virtual mesh interfaces and they should ideally join separate mesh network.
AP1 AP2
ap1-mp2(mesh-ssid) ap1-mp2(mesh-ssid) Successfully connected
ap1-mp2(mesh-ssid1) ap1-mp2(mesh-ssid1) Not connected
ap1-mp2(mesh-ssid2) ap1-mp2(mesh-ssid2) Not connected
ap1-mp2(mesh-ssid3) ap1-mp2(mesh-ssid3) Not connected
Attached is the file u can use to replicate. Also attached is the wireshark capture file.( AP1_AP2_MAC_changed_multi_MESH_2)
On the wireshark packed you can see all the virtual interfaces sending their beacon's ( for example from packet number 13 to 20). Of all the mesh interface only "ap1-mp2" and "ap2-mp2" connect.
Note: On the wireshark file (AP1_AP2_MAC_changed_multi_MESH) the MAC address is different from the program as I manually changed them after running the program, as a MAC address like (02:02:00:00:00:09:00) seems to be reserved for MS-NLB-PhysServe. Though I think it should cause no issue.
Regards,
Manash