Yes, it is. The made their own decisions and had the freedom, funding and resources to do so. If they design themselves into a broken, poorly implemented or non-functional corner, it will be Entirely their own fault.
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...they want to make a 3D world when D&D is made for a flat one.
No, it isn't. Nothing about current D&D is made for flat worlds, at all. Boring DMs may design their spaces that way, but it's not a fault of the system and the system is in no way designed towards flat worlds. It handles unusual terrain and 3D environments perfectly comfortably, and with no more difficulty than a flat or land-based set-up.
