Names and numbers... you're assuming that Bay's Transformers movie scripts are meant to make sense.
The plot holes are big enough for one of those ships to fly through...
It was one of the benefits of John Barber using the comics universe to fill in the plot holes of the 3 movies.
You actually need to read the TF3 comic adaptation before you see the movie, to make sense of the story while enjoying the special effects.
Even the ending in the comic made more sense (Megatron redeems himself in the comic and is allowed to go free).
(Bay's movies are basically a series of special effects shots that he visualises in his head, patched together to create a movie, that ends up being rather disjointed or failing to make sense altogether)