Because it is the only intuitive way to refer to them.
They are obviously female-ish looking.
So you can't call them "he".
They are people, so "it" would be really rude.
Any non-standard pronoun would lead to rejection from the viewers.
They are as female as transformers are male.
That is, they are conforming to a human gender because humans don't handle exotic identity concepts well.
We instinctually shove them to male or female, if they are in any way anthropomorphic and/or sentient.
Also it makes voice acting, marketing and writing much easier.
Just imagine you had to wrap your head around a completely neutral xi/xir concept that would have to avoid typical male and female behavior, even all human behavior.
You would need to set and defend against flanderisation an ironclad standard of behavior and mannerisms, filter for human gender expression at every turn, push the fact in your marketing to ward against confusion, and then you would need voice acting that emulates a third gender distinct from male and female alike.
And then you would get panned by the viewers for your shenanigans because they can't empathise with your characters now and you pushed that fact so far to the forefront that it tints everything about the show.