Could I build a min-website modules without hosted it under Kooboo? Since I would like to use the .NET to design the layout.

Yes, a Kooboo module is an stand alone application. It can be inserted into Kooboo as a module or can run by itself just like a regular ASP.NET MVC website. 

Thanks.

Then, could I host it alone as a single instance and utilities admin function from Kooboo?

I think the answer should be YES.

But do you mind posting your question to http://forum.kooboo.com instead, we are not monitoring the forum here.