This answer requires a deeper study of the Islamic Principles of Jurisprudence (Usool al-Fiqh).
First aspect that needs to be addressed is the fact that a Rasool is to be obeyed until the end of Time. One of the proofs for this is the verse:
"And We did not send any messenger except to be obeyed by permission
of Allah." [4:60]
Every messenger was sent to be obeyed, so this means we must obey our Messenger even after his death (sal Allahu 'alayhi wa sallam). More proofs can be furnished on request.
I want to make sure we are on the same page here, as this is a tenet of Sunni Islam to obey the Messenger. From this point on, instead of saying "order of Messenger", I will say "orders of Islam" since in Sunni Islam an order from the Quran and Sunnah are one and the same.
As for the 3 possibilities you have mentioned, they are all possible depending on the context and command.
When you see a command of Islam, the default is possibility #1. Like I said, this requires a deeper study of Islamic Law, but I will mention one example from the linguistic point of view (linguistic proof):
When your parents ask you for a glass of water, are they asking for it now, or next week? And is the glass supposed to be half full, or full? If you don't want them to be angry, you give them a full glass immediately. These are assumptions that can be inferred from their command.
Likewise, when you see an order of Islam, there are certain assumptions you can make. Since Islam is a religion for all mankind until the end of time (See 7:158), we can assume that the order is going to be absolute (not change) until the end of the time. For example, prayer, Hajj, sacrifice, fasting, etc.
If there is a command that is general (no specific details) or refers to what is المعروف (what's known as custom), then the specifics can change from time and place. For example, how much to give in dowry for marriage, give in charity, how exactly to be good to your parents, etc. The Quran says to give according to custom (this is a clear indication), so that can change according to time and place.
There are a few instances of orders that the Prophet gave which had a time-limit to it. One such topic is temporary marriage (المتعه), which the Sunnis say was a temporary command (while our Shia brethren disagree). Another less controversial example would be the Prophet commanding not to pray until reaching a certain spot in an expedition (hadith is in Sahih Bukhari).
Regarding example #1, it is actually not an order (obligatory) but recommended to use the miswak. One of the proofs is the hadith in Bukhari:
Allah's Apostle said, "If I had not found it hard for my followers or
the people, I would have ordered them to clean their teeth with Siwak
for every prayer."
Since he is saying "would have", it is not a command of obligation. In any case, a plastic toothbrush is arguably better than a wooden toothbrush (in terms of physical cleanliness) but you can still use the wooden toothbrush out of love for the Prophet and a desire to emulate him (basically for spiritual reasons).
Regarding example #2, since there is no indication that we are to give anything other than 2.5% (and all the detailed rulings regarding Zakah), the command is absolute. There is no indication that this percentage was chosen in consideration of economic conditions, or any indication that this is open to change. If there was, then maybe we could say something.
Finally, it is incorrect to say that Allah has not given detailed rulings on Zakah. It is true that there aren't detailed rulings in the Quran, but Allah through his Messenger has given many detailed provisions on Zakat. Just look at this Chapter on Zakah for example.