It helps here, as it often does in English, to consider the etymologies of the words. Their contemporary usage still echoes their Latin roots. Below, I will provide links to a dictionary that provides especially convenient etymologies.
temporary comes from the Latin word for time. It means "for a time". The related word temporal is just an adjective for "time". Here are some phrases where people say temporary:
a temporary appointment: An appointment for a short time, shorter than the normal duration. For example, at colleges, the dean is normally appointed with the expectation that he or she will serve many years. Sometimes it's hard to find someone willing to make this commitment, so they might settle for a person willing to serve as dean for, say, six months, while the college searches for someone else to serve permanently.
temporary housing: Housing that the residents intend to stay in only for a brief time before moving to permanent housing. Refugees fleeing a country, or people whose homes were damaged by a hurricane, or a new employee coming to work in a new city might stay in temporary housing for a few months until they find a home of their own or their permanent home is repaired.
Usually, though not necessarily, when something is done temporarily, there is a definite expected time when it will end. For example, the dean is appointed for six months, instead of the usual longer duration. If there's no "expiration date" known in advance, the time is expected to be brief. The notion of time is felt very strongly when people say "temporary".
provisional comes from the same Latin root as vision, meaning "looking". The pro- part adds the notion of "looking after" something (taking care of it) or "looking ahead" (exercising foresight or caution). Provisional has connotations similar to the sentence "We'll see." When people say that something is done provisionally, usually they mean that they will "keep an eye on it", because they're not yet sure if it's suitable to be given a full or permanent responsibility or because it's not ready yet. They are acting cautiously, refraining from committing to the new thing, at least for now.
A provisional appointment is one made with the intention to decide, at a later date, whether to extend it or make it permanent, based on how the appointee actually performed.
A provisional driver's license is granted to a young driver before they are old enough to qualify for a full license. Usually a provisional license specifies that the driver may only drive if accompanied by a fully licensed driver. The fully licensed driver is expected to watch over the new driver as they drive, providing guidance and helping prevent accidents. After a time, the new driver will be allowed to apply for a full license.
There is a lot of overlap between temporary and provisional. You were right to notice it. A provisional government is a special, temporary government made to get a country through a crisis—such as the birth of a new country following a war. When the crisis is over, a normal government is expected to be appointed, perhaps after the country adopts a new constitution. The difference is that provisional emphasizes caution, uncertainty, and "looking after" or taking care of the fledgling new country until it's able to function completely on its own. For some more insight, compare the word "provision".
Hopefully it is now clear that provisional is a much better word for scientific theories than temporary. Calling scientific theories provisional means that they are not conclusively proven by the evidence available at the time they are proposed or accepted. We have to keep looking into it. We may discover new evidence or new reasoning that leads us to revise or reject the theory. It's the best guess that we have now, though, so we accept it provisionally. "We'll see."
transient comes from Latin roots meaning "going across". The trans- part means "across", and appears in many English words where that is part of the meaning, like transportation and transitive. "Transient" suggests rapid movement, something that stays or exists only very briefly, maybe almost instantaneously. It's often used as a noun. For example, an electrical transient is a momentary surge in voltage in an electrical circuit. Homeless people are sometimes called transients because they don't have any reliable place to stay for even one night, so they might "move" someplace new almost every day. As an adjective, see this article in Merriam-Webster's Dictionary of Synonyms. Notice that the synonyms compared there do not include temporary or provisional. The speed or fleeting duration implied by transient led the authors to group it with other words that also suggest lasting or remaining only a moment.
We hope that most scientific theories aren't transient. That would suggest that they are adopted and rejected very quickly—maybe holding consensus for only a day or a week. Usually when people call something "scientific", they mean to attach some authority to it. Even though it's provisional, people expect that a scientific theory should be based solidly on enough evidence that it's not likely to be overturned before tomorrow morning.