do you know if the plugin would touch the Apache configuration?
No it doesn't change that setting. It can't in fact.
Are there any detailed documentation available (for setting up W3TC) ?
I don't know what to say. I have 3 choices: 1. Remove all of the options and force people to optimize their sites as I desire. 2. Leave the options, keep reasonable defaults and let users read the captions and make their own discoveries. 3. Do #2 and write a 200 KB FAQ instead of my 100 KB one, trying to answer every conceivable question before it's asked. Basically write a book.
I've chosen some of #3. I try to update the FAQ as I can.
One other thing that I've been noticing, wp-content/w3tc/ has permissions that exceed any that I have via FTP or CPanel.
I don't know what this means.