1. This verse is related to prostitution as is evident in the WOMEN being specified. They are the ones who primarily have indulged in this act. This is also supported by the fact that in the next verse, the punishment regarding both males and females who commit zina is related.
2. The Quran gives a punishment that they be confined to their homes, as to protect society from their lewd activities. This was a temporary injunction, "until Allah ordains for them another way".
3. Rape is not adultery, nor are 4 witnesses required. Adultery is when 2 CONSENTING adults have sex. Rape is fasaad and corruption, and the state would be in a position to gather all the evidence necessary, including medical examinations. The injunction of 4 witnesses is primarily meant to PROTECT the honour of the accused of adultery.