The having a choice to pick name from the 100+ or so games i play i maybe found 5ish and now yours that i couldn't pick it or at least change it myself since the files where .rpy which is easy to fix and while i can already tell its not the generic throw away character a lot of devs use, picking a name is more of a bonus for those that want it and an easy "i recommend using the default character name or some cutscenes might have your chosen name" warning would be a compromise. and the [MC] is just a standard renpy command that uses the defined "MC" and displays whatever name it has since i did take a look at your code and saw you had typed out "Lyra" instead of [MC] which works for any character not just the mc for those with longer names you can use their version of [MC] to lessen your work load while also removing the risk of you misspelling the characters name as i seen other devs do way to often when not using that system.
in the end its more of a compromise some cutscenes might not say the players chosen name as they are pre rendered with text so a short warning telling players its better if they stick with default but its a forced you dont have a choice type of deal would be the middle ground.
I completely understand the focus on EP 3 as well but i also gotta warn if you are thinking about letting players choose i wouldn't wait to long as restarting a save might be needed and moving code around often break save files as well for those that don't really care, just something to keep in mind.