It's done all the time. All you need is a transition strip. However, it's not really a big deal to remove all of that either if done correctly. Putting additional height directly affects the kitchen design as it impacts the floor to ceiling clearance and that affects your appliance installations and overall height of the cabinets. If this is a room that started life with only 8' ceilings, you may be down to 94" or less. You may have to do a soffit or built up crown to get things to work correctly.

The cabinets go on top of the finished flooring, and it's always best to start with the bare subfloor first.