When you rename your starting characters in FTL, are those names added to the default list for later games

Added in v1.54, the Advanced Edition. Changelog:

Rename mid game: Rename any crewmember from the Crew Manifest screen

According to the FTL website, the coming expansion, FTL: Advanced Edition, will allow renaming of crew mid-game. Coming in "early 2014". Keep your eyes peeled!

Yes, it is possible to change the list of names. Do note that names in the game were a $100+ backer reward on the initial Kickstarter.

At any rate, you will need to unpack {FTL root}/resources/data.dat with a tool such as ftldat (ftldat unpack path/to/data.dat). Once unpacked, you will find a file called {data.dat unpacked}/data/names.xml.

You can edit this with any text editor (it does use Unix linebreaks, though, so you might want to refrain from using notepad.exe) to change the list. You will have to follow the same conventions the game uses, but other than that, anything is possible.

Once you're done, back up your original data.dat, repack it with ftldat (ftldat pack path/to/data.dat) and you're good to go.

As for the conventions in the names.xml file.

A list is wrapped in a set of <nameList race="{race}" sex="{sex}"></nameList> tags, where {race} currently seems to have no effect (or at least "human" is given to all races, no matter what. Entering another race, such as "engi" might restrict it to that given race.) and {sex} can be either male or female.

Inside the nameList tags, each name is to be added as a <name short="{short}">{name}</name> tag. Here, short is an optional attribute, but it is used to shorten names that are too long for the UI. When {name} includes spaces, only the last section is used ("Sir Jonathan Kirby" results in "Kirby"), unless a short attribute is specified.