How can the Prophet's prohibition against holding urine in a basin at home and the fact that angels do not enter such a place be reconciled with his action of placing a urination pot under his bed?

There is no contradiction between the two hadiths. The first permits urinating into a vessel and leaving it overnight out of necessity, while the second forbids "naturally soaking" (naq'a) urine, meaning leaving it for a long period. This is how the people of knowledge have reconciled them.