These are interesting comments and Sebastian is quite accurate in his explanation as is Clay, but I'd like to elaborate a little on this.
I work and have worked with the site wizard extensively for the last 3 years, in fact, created those little templates you see (business, club, personal) under the advice of Shaun when Vicenc first wrote the documentation, and so it could be put into the build in DNN3. I feel that the site wizard is very underused, even inspite of it's shortcomings.
A portal creator is completely different and there are 'portal creators' around, I believe Onyaketch has one, and I know Armand has one being written with Juna and I have one that was writen by Armand on a DNN3 Platform and the behaviour of a portal creator steps you out side the functionaliy of the template creator.
There are some shortcomings I've seen with the template creator and I don't know how or if they will ever be addressed since there are complexities in DNN that I'm finding on a regular basis that might not be by design, but things that are discovered on the way.
For example - I have many templates created which I use to run my sites, my client sites, my ecommerce, my reselle websites, and in particular, have found that modules that require further functionality within the 'module settings' or are highly customisable at page level really don't take to being exported in the host/portal export template function too well.
I do make use of the module settings in many sites to find that they are not carried through to the new portal, particularly the links module - which brings up wrong tabIDs and the catalook store which allows customised functionality on each module which has to be redone once it's exported and imported again.
Having said this, once you study and understand how the site wizard works, how DNN allows the copy/reference/new functionality, import/export of modules, you can replicate a site fairly quickly, even if it does require going into each page and making some quick changes. I know it's not the perfect solution, but if you're working with modules you know have alot of extra 'module settings' that pertains to the mdule (you know when you click the 'module settings' and you get some extra features on the modules) you can build the majority of your sites locally, then choose to finish them live, unless you do as I do with some clients and that is to create the whole site locally, zip and upload to server, including an 'attached' copy of the db and then get it running from there.
Personally, I think if I'm doing sites with a range of modules that are not core, then I would be testing their export functionality.
Putting your skins in the _default folder will always make a smooth transition and any of those ugly errors that come up are quickly removed by simply using FTP to copy the files up or using the skin uploader.
At the end of the day, DNN offers a different way of doing things by comparison to what other products do, and I'm telling that having worked on a joomla build, a zen cart build and an xcart build over the last 2 weeks I'm confused as how they work too. Learning this application is done through using it and testing it, and it seems that you've already started to, but perhaps rather than asking for things to be changed to suit, learn to change how you approach things and your 'master templates' keep getting better and better.
I'm really happy the schema was fixed for the templates since it was broken for some time and I really missed using this feature and hope to share with others, how cool the templating functionality of DNN really is.
Hope this gives you more insight to how to work with this feature.
Nina Meiers
My Site - My Blogs - Goodies - 28 Free DNNSkins - Nina's Free Skins