Hi,
I have found the solution if someone should came accros the same problem.
So the solution is to use powerShell and specify the CA to use:
here is the example.
Set-VpnConnection -Name "My VPN Connection" -MachineCertificateIssuerFilter 'C:\mycerts\cert_export_MikrotikIKEv2-CA.crt'
Now I can have multiple IKEv2 VPN Clients on my Windows Machine.
Maybe an WiKi Update would not be also good because lots of people are using IKEv2 More and More!