From all the attached pictures, it looks like it's the handle on the coffee cups that's giving you the problem. The cup holder above should work just fine. The extra gap looks like what's in the front console in one of our cars. The depth is the same as the car's cup holders. You'd have to do a little modifying to the couch arms get get the cup holders recessed.
Just a thought, Have you considered getting some of those handle-less ceramic travel mugs? I know Starbucks sells them.
I would search for things like custom boat console/furniture, or marine seating, etc.
Ah, alas. Might be easier to find a different coffee cup. ;)
Check you library. Our campus library has a 3d printing service.
That's not a bad idea. Some public libraries have ones you can rent, if you find a design on Thingiverse, or something. There are also public maker spaces around that have 3D printers.
Just need to make sure its one that has a large enough build area for your needs.
Couches are for dogs and lazy teenagers.
Men stand when drinking their coffee :)