The decision between "could have" and "could" really isn't about whether an action is a single occurrence or repeated. It just depends on your intended meaning.
"Could" in this kind of situation really has 2 possible meanings, similar, but sometimes subtly different.
#1 past tense of "can" [E.g. "He gave what he could give."] This "could" tells about someone's ability/capability in the past.
#2 expressing a shade of doubt or a lesser degree of ability or possibility [E.g. "It could be so."] This one is for speculating about the likelihood of an event happening (or not).
It is rather confusing that the past tense of sense #1 looks just like the present tense of sense #2.
#1 [can/could; someone's ability]
present: "He can swim." [He has that ability]
past: "He could swim." [He had the ability at that time]
#2 [speculating about something happening.]
present: "What should I do on such a beautiful day? I could swim out
to the island and get some exercise." [I might do that]
past: "Where did Arthur go? He could have swum out to the island for
some exercise." [Maybe he did.]
So addressing your examples:
1) He could start a business in the nineties.
2) He could have started a business in the nineties.
Either of those can be right grammatically, depending on what you mean to say. The first one is about what he was able to do. It says that in the nineties he was capable of starting a business. (And perhaps he did.) The second one speculates about what might have happened in the nineties (He might have started a business. But since the discussion remains hypothetical, even though the nineties are over, the implication is that it didn't happen.)
Your original example is similar except for some extra context.
The siblings lived with abusive parents. They could run away anytime
if they wanted.
That last sentence tells us they could run away if they wanted. Since it speaks of an event in the past which remains an 'if', we would probably assume that they didn't do it (because they didn't want to).
So I feel that the statement should be interpreted as in sense #2. In other words it is about a past event that might have happened (but it didn't). So the verb should be "could have run".
The siblings lived with abusive parents. They could have run away any
time if they wanted.
The other interpretation could also be valid, if you just want to state that they had the ability to run away whenever they wanted. In that case my preference would be to lose the "if":
The siblings lived with abusive parents. They could run away anytime
they wanted.
But the whole statement sounds less likely that second way, and I don't think that is the intended meaning.
Note that the two uses of "could" are closely related. Many situations are about both someone's ability/capacity and speculation about something happening. So it often doesn't make a bit of difference which sense you choose for your statement.
In cases where it does matter, people fluent in English will know without thinking which "could" they mean, and they will select the verb tense accordingly. But if you ask us to say why, then we try to figure it out, and we get so confused, we often come up with bogus reasons, such as: "It's because it's a single event vs. a longer time period."; "We don't use 'could' in a positive sentence when referring to a single occasion."; "You only say 'he could have' if he didn't."; or "The words just flow better that way."
Some of those explantions could be valid in specific examples, but the real reason (in general) is this: If you are talking about the past, "Could" is for someone's ability or capacity, and "could have" is for discussion about something maybe happening (or not).
Formal definitions for "could" used in sense #1 and sense #2 are given by https://www.yourdictionary.com/could as definitions 1. and 2.a. respectively.