it is the place(where)they once lived it was in the place (t

it was IN the place that they once lived等于it was the place that they once lived IN ,把第二句和
it is the place where they once lived 比较下.
你会发现含that的句子多了一个 in,where 是地点代词所以只能指代place；that是综合性的,无论啥都可以指代.所以你列的第一句中where,that,which都可以用,第二句只有在that,which中选了.

第一句中where引导的是定语从句修饰the place. 因为place是表地点的词所以用where引导定语从句
第二句是强调句型，其结构是“It is/was +被强调部分+ that/who+其他部分”，其中that前面接的是事物，who前面接的是人。本句中被强调的是in the place,指事物，所以用that....

第1句是壮语从句，第2句中是用it 和that引导的强调句