Holy shit are you guys paranoid.
I don't how you lot don't understand how WMT actually works.
WMT isn't a tracking tool like Google Analytics, where I understand the paranoia can come from. When you set up WMT and you're asked to verify your website, it's so that Google authorises access to information they've collected about your website. The moment your website is indexed, Google starts to collect information about your website, indexed pages, impressions, clicks etc. So you verify your website to say show that you can access that information for a particular website.
So if you think you're being clever by not verifying that information, then you're being extremely stupid.
If you're running large blog networks, then sure as fuck don't create that pattern for them. But Considering you're struggling to get a website indexed then I feel that you're not at that level just yet. If you're scared about that sort of stuff then with each domain just create a new account.
Google isn't blind to your website until you verify your account