You think female Shauna was the canon choice? Hahahaha. Sorry, that was just too funny. On both paths Shauna has severe body dismorphia. For a trans person, that makes sense. On a cis person, it doesn't. Then you have Penny. Penny became a fan of Ethan before she met him because of the stories of how he helped Shauna accept who she is and protected her from the bullies. Ethan then suggests Penny and Shauna should be friends since they have something in common. If they are both trans, then that makes a lot of sense. If they are both cis, the fact they were both bullied is a very weak reason to become a fan and friends with a woman she has never met. The one thing you said that is actually true is that Ethan has realized he is somewhat bisexual as the game has progressed when he had sex with Skye. Ethan cares about the person, not what is between their legs.
Ohh, and, if you look at the game files, there is a variable at the start of the game called shaunafemale. By default it is set to false. During the dialogue where you select if Shauna is female or trans, you will notice the only time something changes with the code is if you choose female. Trans Shauna was and still is the default. Since Penny's gender identity is based on Shauna's, Penny being trans was and still is the default too.
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