中国人：你的中文是[在哪里]学的？ indicates the question is asking 'where'

中国人：你的中文是[怎么]学的？ indicates the question is asking 'how'

中国人：你的中文是[从哪里]学的？ indicates the question is asking 'from what source'
And sources include locations and objects'-- For example: from books, from classes, from T.V. or even from my father's one on one teaching. And that's in effect, asking 'with what methods'-->  'how' you learn Chinese

When the Chinese person asking '在哪里学的': 

'哪里' can refer to 'what location' e.g. Hong Kong, Beijing, Shanghai. 

'哪里' can refer to 'source' e.g. books, classes, the internet.

>Does 「你的中文是在哪里学的？」mean “How did you study Chinese?” or “Where did you study Chinese?” 

It can mean either. 

在北京语言大学学的。 or  在(北京大学的)語文班学的 are both valid answer