that改成who 就可以了

不可以。
应该改成：This boss whose company my father worked in many years ago is a very kind man.

可以用This boss whose company in which my father worked many years ago is a very kind man.

不可以。但需要说明的是that是指同位语。一楼的也可以。

This boss in whose company my father worked many years ago is a very kind man.