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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Ok, I am not going to argue that there is a canon option for Shauna one way or the other.
I do however have to point out that from a developer viewpoint, the argument that the Shauna trans route is canon because the begining game variable is set to shaunafemale = False, is complete garbage.
As a dev, when you code a game, the items you define with a default of "False" are the changable variables of the game. The lable of "False" is a default setting prior to a specific variable occuring. These variables are either things that have no real impact on the game and are mainly player preference, or they have a major impact in the game and on occasion the game can not progress until the variable has been set to True. Sometimes these occur due to player choice, sometimes they occur as a result of normal game play. As a dev, 99% of the time the desired outcome is for the variable to be changed to true in order to progress the story.
To see evidence of this, look 2 defaults below the "default shaunafemale = False" statement and you will see "default shaunalove = False" If the argument is that Shauna Trans is canon because the default status of shaunafemale is false, then, by the same logic, it would stand to say that it is also canon to say no to Shauna.
As I said before, 99% of the time, the canon variable is the one that when selected becomes True. Numerous games begin with all of the options regaurding LI's set to "False" because the player hasn't reached that part of the game yet. Once they do, the variables change to "True". It would be ridiculous to think that in all of these games the canon route would be for the player to never meet any of the LI's just because the variables of having met the LI is set to False at the outset of the game.
This argument is a logical falasy. Most likely BD made the option for Shauna to be trans available because he wanted to include trans content in his game and so made it an option. Personally I don't really care either way. I have my preference and others have theirs, and that is fine. As a Dev, I just had to point out the error with this specific argument.