Hi, Just a thought.... we have a french lop that is free range, Billy. He has a large cage in our living room for bedtime and when we're out. We use a cat litter tray at one side of his cage, with a good wad of kitchen paper in the bottom. On top of the paper, I put a layer of straw... uncut and then hay. He poops one end and eats from the other ! There's newspaper on the cage floor, in case of any mishaps.. easy to pick up and change. Have done this for nearly 20 yrs with one bunny or another... NO smell. I change it fully every day... but you can just lift off the top layer of hay / straw to re-use, get rid of the yukky bits below, then just change the paper. Wipe the litter tray out with a good bunny disinfectant such as Johnson's every day before you put the clean kitchen paper in. Only takes 10 mins.. even with a bunny helping
Cleanliness can be the key... the cleaner it is kept, the cleaner they keep it. Billy and my others love a clean box... he boings up and down on it for ages, ferking around to see what he can find. And I clean his cage properly once a week. Only takes half an hour, obviously under Billy's watchful eye!
Also what you feed them can affect the smell. Billy has good quality hay... two or three different types for different flavours which he eats a lot of... and then Burgess Excel granules. He has a little celery, a small slice of apple at bedtime, the odd slice of tomato.. with pips removed... and I collect grass and dandelions from the garden. That's pretty much it.
Not sure if any of this helps, but it's worth a thought
Good luck,
Nette