If you create a custom object in Marketo and link it to lead and contact with 2 lookup fields, you will not be able to use this dual mapping in Marketo to create 1 custom object mapped to not leads and contacts. This is just not possible as Marketo sees this twin relationship as 2 SFDC distinct custom objects. Furthermore, if you try to map them both, you will get an error, because they have the exact same name.
It should be possible to create one Marketo custom object out of these 2 relationships, and make Marketo smart enough to detect the lead conversion and "follow" the change in the linked fields.
Ideally, Marketo would even be helpful, when a lead is converted to capture the ID of the resulting contact and update the relationship field in the custom object instances so that the link is set to the resulting contact (this currently requires the development of some painful SFDC triggers).
The same mechanism should also apply to custom objects mapped to lead and account
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