Your intuition is right. There is no grammatical requirement of tense agreement between the main clause and its dependent clause. In each clause, you simply choose the tense which conveys the intended meaning. So in your example, "has" would be used if the system now has the potential. "Had" would be used if the system had the potential but does not now.
I should clarify that there are limitations on what tense you can use in some types of dependent clause. For example:
I will let you know when I am ready to be picked up
*I will let you know when I will be ready to be picked up
*I will let you know when I was ready to be picked up
Of course you could argue that these are, in a sense, errors of semantics – that they are grammatically correct nonsense. The second example would be perfectly acceptable if what you mean is that at some point in the future you will announce to your friend the time at which you will be ready. The third example would be perfectly acceptable if what you mean is that at some point in the future you will disclose information about a time in the past when you were ready to be picked up.