The reason for the portalAlias table is so you can host multiple sites under one instance of DNN.  For example you can have mysite1,com, mysite2,com, mysite3.com and they all point to the same IP address.  In IIS the IP is used for one web site or VD.  Then when users hit the site it loads the correct content based on the URL used (aka: PortalAlias). 

Not sure what the PortalAlias table has to do with whether it can be run as a WSP or WAP application.

As far as where in the questions about where in the code it prevents direct use of appliation name from browser request and where is the code to adding port numbers I would have to look at the code to find that out.  I am not really sure what you are looking for, so not sure I can help you on that front.  But, since this is open source you have the code so you can search for it just like anyone else in the community could.   As far as I know the code does not add port numbers, but if you have a port number in the URL you access the site with then the URL with port number has to be in the PortalAlias table and the <usePortNumber> set to true in the web.config.

I would also highly recommend that you do not update the core code.  If you do you are just asking for troubles when you upgrade, since you will have to re-incoporate you changes each time you upgrade to the latest version.