For CIs coming to RTSM from OM topology integration there is no such thing as default KPIs. In the OM->BSM integration scenario (actually in any integration scenario that is based on events) KPIs are assigned to a CI if and only if there are events resolved to that CI or any underlying CIs (in this case KPIs are propogated from child CIs). Every event is supposed to have ETI that turns into HI on BSM side (in case it's a health contributing ETI). So if HI in its turn is configured to contribute to a certain KPI, that KPI will appear.
In other words, KPI only appear if there are events coming with corresponding ETIs/HIs. You won't see any KPIs till such events arrive into BSM.
I don't know why you see the same HI affecting both System Availability and System Performance KPIs. The system I work with (BSM 9.10) shows different HIs for System Availability and System Performance KPIs when I check KPI Assignment rules for Computer CIT (Admin->Service Health->Assignments->KPI Assignments).