Design=Choices.
You have provided some pretty vague issues so I think you’ll need to provide a little more specific information.
1) Sure it can be removed, along with the functionality it provides.
2) How do you not have a need for a page layout of some sorts?
3) Depending on the original design it should be able to be ported or referenced from DotNetNuke.
4) What can’t be rendered?
5) What features?
6) Ok.
Since all projects are modules under DNN, you really don’t need to modify the core. Any competent programmer can manage the framework in a relatively short period of time. So far, your requirements do not specify why you could not use DotNetNuke in the first place.
It sounds to me like you would like a highly customized system with no page formatting, that has to be unaffected by advances in technology or upgrades, and it should work out of the box.
If your budget is between 6 and 7 figures, you might find a solution some day. Or you can have DotNetNuke up and running in a few hours for less then the cost of your morning coffee.