Is it obligatory to always place books containing the name of Allah the Almighty on top, or is it permissible to place books that are not from the Sharia sciences, such as mathematics and physics, on top of each other in any order?

It is difficult to enumerate the instances where Allah is mentioned in these books, and doing so might be an unnecessary burden, so do not preoccupy yourself with that. Some scholars have permitted placing Sunan books on top of the Mus'haf (Qur'an), but it is more appropriate to place these books on top of each other, as they are not primarily intended for religious knowledge or remembrance [of Allah], but rather mention [of Allah] occurs in them incidentally. We advise you to abandon such over-exertion, as it might lead you to obsessive thoughts (waswasah).