What makes it custom is having the design fit and reflect 'your' space. Any obstacles in the flooring/walls/ceiling are addressed in the cabinetry to make the Space look seamless and natural.
Getting a custom kitchen also offers the possibility to get nice features or accessories to make using the space easier and more pleasant. Think of more accessible corners, full extension drawer systems, pull out cabinets, and decorative finishes. There are many variables that play a role in giving a kitchen the wow-factor, so make a list of what. Is important to you, and work closely into those details with your kitchen designer

There are many factors that make a custom kitchen unique, but most important is thoughtful design and careful planning. I typically spend more time in the design phase of a kitchen than I do in the production. That said, inset doors is by far the most custom detail aesthetically. I also like a ''built in'' look and custom moldings whenever possible. Of course this depends greatly on your style.

They say beauty is in the eye of the beholder - so we experts listen very carefully to what the client is hoping for - and then we do our absolute best to make this dream a reality ! It's what most of us have a passion for - so that, thankfully, is usually a joy to do !!!
Top tips - create an Ideabook of all the things you love to see in a kitchen and ask your expert to include these, if they can, in to a design done specifically for you!
Never compromise on safety.
Try not to put looks ahead of usability.
Always imagine using the proposed design to cook and entertain your entire family, and to cook your favourite dish for two.
Use tape to tape out the space on the floor if you can ! It really helps you see just how far the fridge is from the kettle etc !!
If you are trying to design this yourself - without the help, knowledge and guidance of an experienced professional, then read up on everything you can beforehand and ask a professional to check the plans before you have anything made !
Best of luck ! :-)