Well, the blue glow inside the Matrix can't be Prime's spark, since it has an obviously solid, crystalline nature - just look at it when Hot Rod opens it in TFTM, and how Optimus was able to take a piece out and give it to Longtooth in the comics. Also, the Whatever from BW and the Matrix from G1 look to be different sizes and designs. Similar designs, but not the same ...

It's the same as how they don't notice that Megatron can be surprisingly agile [Fire in the Sky, Heavy Metal War]. Basically, comes down to people not looking at the canon and putting all the pieces of data together.