[Manal]

Actually, it shows every DNS list in your Cloudflare.
So for me, I do have domain in Cloudflare, the main domain I used Cloudflare DNS and SSL. But for other domain like the subdomain (cloud.domain.org, damn Cloudflare broke OwnCloud), I don't use Cloudflare DNS and SSL.

Nah, there's why you can see your main IP address.
But, if all of your DNS listed in Cloudflare using Cloudflare's DNS, it will not list any of your VPS IP address.

It's pretty easy to configure by your own, but if you don't understand, I recommend to hire Manal on his Fiverr.

If you try ShadowCrypt's DNS resolver to resolve your website, it will show all your DNS list. But if you use ShadowCrypt's Cloudflare resolver to resolve your website, it will show you Cloudflare's IP pointing to your domain/sub-domain and non-cloudflare IP for the same(if there is any sub-domain which is not configured properly with cloudflare, it is vulnerable to be bypassed).

EDIT :- Thank you for your compliment and recommendation