If there is already another example flying with the configuration that you want, then it could be reasonably straightforward to go on the back of that previous mod approval. Likewise, if you are changing to another configuration provided by the manufacturer (or designer) and convert to that exact specification, then there shouldn't be too much difficulty.
Otherwise, you would need to demonstrate that what you are doing conforms with an appropriate certification code (e.g. VLA ot pt 23) and that will probably involve more effort and expense than you'd want to expend.
Really a lot better to search out the aircraft that is already close to your ideal.