1. For years D has been capable of installing templates as you mentioned in wordpress. You upload the template files, go to your Admin Panel & select the one you up (if you've uploaded it to your server), click save and amazingly it's installed. Unless of course you have tons of mods that apply to the template files and then you MUST adjust your template to match those.

2. Do what the rest of us do, if you want a truly custom look that is NOTHING like the rest of the sites out there then see more hire a designer to do it for you and place it in the contract that it is an exclusive design, hire employees and have them do it or learn to do design yourself and create it.

In the end, the templates are done in the manner they are done because of the issue with if you go to far with a mass template then the vast majority will not buy it as it will screw up their sites when they're integrated into them due to the heavy modding all of us do. As far as integrating the template goes, not sure how much simpler you want Boonex to make installing a new template than it already is. Perhaps it'd be good if they also made it upload itself, do the switching and all without you even logging in.