In this following sentence:
The boy is running?
Is the word "running" a gerund? If so, why does this make sense? Why does the sentence structurally make sense?
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A gerund is a form of a verb used as a noun, whereas a participle is a form of verb used as an adjective or as a verb in conjunction with an auxiliary verb.
In English, the present participle has the same form as the gerund, and the difference is in how they are used.
In the case of your question, is is an auxiliary verb and running is a present participle.
The boy is running.
The sentence is in the present continuous, in which the word running has been used as a present participle, not as a gerund.
The word running as a gerund means the action of running. You can say "The boy likes running", "Running is his hobby", but you cannot call a person running. In other words, It's nonsensical to say "The boy is the activity or action of running".