Is there anywhere that they were originally announced as being two seasons? From what I remember of the official announcements (press releases and at BotCon), they were always noted or referred to as a single season/series, as they were always announced as one-off series/seasons of 52 episodes... and I've hardly ever heard of them being referred to as two (even by fans).

Even Beast Machines was a series of 26 episodes, screened during one Television season (Sept 1999 to May 2000)... but some (vocal) fans later split them up into two seasons, purely based on them seeing the standard feature of Hasbro adding a sub-title to their toy packs in their second year of most lines since Beast Machines, to help convince Retailers to stock the same toyline for a second year.

Battle for the Spark (Beast Machines), Unicron Battles (Armada), Powerlinx Battles (Energon), Primus Unleashed (Cybertron), Allspark Power (2007 Movie), Hunt for the Decepticons (2009 Movie), Movie Trilogy (2011 Movie), Beast Hunters (TFPrime), Energize (Rescue Bots)... even though some were incorporated into their applicable show/movie later, it was created just to sell the toys to Retailers first.