There's nothing hard on reading/writing booleans from an XML file, as long as you do it properly:
Writing:
code:
node.text = 1*bBoolean;
Reading:
code:
bBoolean = (1*node.text == true);
That way, you always read and write 0 or 1 and you don't have to worry about converting a string containing "true" to a Boolean and such.
However, if it's for keeping a user's preferences, I'd recommend using the registry, yes. It's easier for you, the developer: no need to create extra files in places where they may get lost, preferences are properly removed when script is uninstalled and the functions are lots simpler. It's also better for the user: he/she won't easily delete them accidentally.
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