Okay, been at this for a couple of hours now...
Bearing in mind we're talking hypotheticals of mating inconsistencies of fact with that of proposed ideas to create a sensible continuity that involves Vector Sigma + Key and the Transmetal Driver...
(Involving the G1, Beast and Transtech eras)

Here are my thoughts so far on the 'Cybertronian Evolution of Reproduction' that is designed to create an effective Timeline and Meshing of continuities which will hopefully solve more issues than it creates and, as with science in general, is open to suggestions, amendments and corrections:

• 13 Primes endowed with ability to reproduce, method is Budding
• Budding:
- Mitotic method
- 1 offspring per bot (Primus’ Will).
- Pre-determined population limit (Primus’ Will).
- Pop limit communicated to each prime subconsciously.
- Pop limit countdown communicated on genetic level through CNA.
- Procreation past Pop limit results in by product (The Swarm).
- Resulting offspring referred to as 1st Cybertronians.
- CNA derived from parent Primes and handed down to each child Cybertronian.
- CNA housed in Laser Core (Proto-Spark).
- 4 Primes (Initially) required, surrounding 5th in circle.
- Chant is enacted, causing massive electro-magnetic, radioactive discharge.
- Bubbles and lesions of liquid metal form on central (5th) robot's chest.
- Process grows more intense, final massive discharge, large mass of liquid metal bursts free from chest, slowly forms metallic-humanoid blank figure (Protoform-esque).
- Offspring solidifies into full Cybertronian.
- Newly born Cybertronian exists only within singular universe (The 1st Universe).
- Cybertronians able to perform Budding until pop limit.
• Budding Population Limit met.
• Primus enters Dormant state (Cybertron).
• 13 Primes become Cybertronian council.
• Cybertronian Council and select Cybertronians granted access to Vector Sigma.
• Vector Sigma:
- Resides in Spherical Chamber deep within Primus (Cybertron).
- Pre-dates 13 Primes.
- Unfathomably powerful, Multiversal Super Computer.
- Core of Computer is ‘All-Spark’.
- Key required activation (Key to Vector Sigma).
• Select Cybertronians overseen by Council, use Vector Sigma to develop Transformation ability upgrade.
• Select Cybertronians overseen by Council, use Vector Sigma to develop Protoforms, ‘True’ Spark and Infusion Reproduction.
• Protoforms:
- Consists of free-flowing, metallic matter layer over basic robotic systems and frame.
- Used as mode for intergalactic transport.
- Transported/Stored in Stasis Lock - Smooth Robotic Humanoid.
- Transported/Stored outside Stasis Lock – Roiling mass of metallic matter surrounding basic robotic system and frame.
- Infused Spark and Alt-mode information required for life.
- Additional use of near instant repair of Transforming Cybertronian.
• Spark:
- Part Donor CNA, part Essence of Primus
- Essence of Primus sourced from ‘All-spark’ Core
- Created by the combination of Vector Sigma, it’s core and key and the Matrix (Matrix of Leadership and Creation Matrix now one and the same).
- Detrimentally reactive to solidified Energon Crystals.
• Infusion:
- Matrix, Vector Sigma (It’s core and key), Spark, Protoform and Alt-mode information required to create new Transforming Cybertronian (True Transformer).
- Spark is generated, placed within Protoform Spark Chamber, resulting Transforming Cybertronian life takes form and shapes Protoform based on combination of Spark and Alt-mode information.
• The Cybertronian known as Orion Pax has Laser Core near extinguished.
• Prime: A3 (Alpha Trion), hearing whispering echoes of Primus, employs an Infusion Reformatting of Orion Pax.
• Orion Pax Reformation by Infusion:
- Prime: A3 places near extinguished Laser Core of Orion Pax, along with own donated CNA into Vector Sigma.
- Protoform and Alt-mode Information then introduced.
- Prime: A3: “Now, with a little hope and a lot of luck…”
- Orion Pax successfully Infusion Reformatted with resulting Spark as Transforming Cybertronian.
- Resulting Transforming Cybertronian is first, 2nd Generation Prime and 14th Prime overall – Dubbed Optimus Prime by Prime: A3.
• 1st Civil War Breaks Out
• Upgraded Cybertronians and Transforming Cybertronians split into 2 factions – The Autobots and Decepticons (Moniker of Cybertronian is dropped in favour of Transformer and/or Allegiance).
• Decepticon Chief-Scientist Shockwave begins Spark Experimentation Program.
• Utilising the research of Shockwave, Decepticon Scientist Jhiaxus begins own Transformer CNA manipulation.
• Jhiaxus genetically modifies Transformer CNA, based on Organic Reproduction studies, resulting in 1st Female Cybertronian being.
• Female Cybertronian Being dubbed: Arcee.
• Jhiaxus’ research abruptly ends, unforseen Meiotic results eventuate…