Shouldn't HOW you're promoting your site play a role in whether or not you use Webmaster? I mean, as long as you're not spamming the hell outta your main site, I don't think it would be a problem?
It`s not a secret that google hates affiliates and MFA websites so in both cases that could result in huge SERP drops/de-indexed websites, etc.
I personally don't trust Google. Therefore, I only have less than 5% of my 100+ domains using webmaster tools.