Beast Wars indeed had protoforms. Those are the "black slates" made of liquid metal that be shaped into anything desirable, done by "reformatting" (reshaping of the body). The very first example of reformatting came from the first Transformers movie of 1986, when Unicron reformatted Megatron into Galvatron.
The concept of Transformers "being born" was never touched upon after G2 (or even Beast Wars) untill the live action movie. But there are some guidelines to "making a transformer" in all continuities:
1. The body, when hit by the energy of a life giving object (AllSpark or Vector Sigma), instantly changes form to accommodate the transformation process.
2. A Spark (or at least a basic sentience) is created or inserted at the same time. Where it comes from nobody knows.
An exception concerns the G1 Combaticons and Dinobots. In the G1 cartoon, they were criminals and had their personalities (read: Sparks) extracted and stored away as punishment. The exiled Starscream, needing an army of his own, retrieved them and inserted them in some army vehicles, which instantly changed shape and transformed.
The Dinobots were constructed by Wheeljack to transform from the very start, in the cartoon that is. In the comic however, they all were original crew members of the Ark when it crashlanded during the Dinosaur era. Teletran 1 gave them the Dinosaur forms they have now.
Bear in mind this all happened before Vector Sigma was introduced

That's basically what I know and theorize.
The resident Rewind... well, half of one

- Jelze Bunnycat =:3
Looking for:
- TR Furos (Hardhead's head) and Crashbash (lost him

)
- PotP Punch head
- TR Galvatron right arm (the gun one)
- CW Brake-Neck/UW Wildrider, CW Offroad
- TR Twinferno & Grotusque
- Greenlight, Lancer and PotP Elita-1
- Legacy Core Slug, Sludge & Snarl