What Paulbot said is correct. Optimus Primal was merely the custodian of Optimus Prime's Spark for a short time, and the power of Prime's Spark did mutate Optimus Primal's body, but the Spark itself remained dormant and separate from Optimus Primal's Spark.

Beast Wars is to G1 what Rogue One is to the Original Star Wars Trilogy -- it doesn't just expand on the original story, it makes the original better.