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"Could" in the first one is just the past tense of "can," as you correctly note. In the second example, you are referring to a possibility in the "farther back" past. "Could Tom's mother have been...
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#3: Attribution notice added
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#2: Initial revision
"Could" in the first one is just the past tense of "can," as you correctly note. In the second example, you are referring to a possibility in the "farther back" past. "Could Tom's mother have been right?" means that you have _the present_ when the story is taking place (even though it's in the past tense) and some incident _in the past_ (Tom's mother accused the narrator of being responsible for Tom's death). If Tom's mother is standing in front of the narrator right now, then it would be "Could Tom's mother be right? Could I be the one responsible?" So both your examples are correct, if the incident with Tom's mother happened at a previous point from the existing scene.