opperating a distillation column far from flooding
Using a much too large column means you loose a lot more heat through its walls, meaning it will take longer for the equilibrium temperature/concentration gradient in it to form, and the destillate comes not only later but also considerably slower.

And you'll have to put more power into heating the still, with following danger of decomposition, unwanted side-products, etc.

If you use an expensive column with silvered vacuum insulation, this effect might not be too large even at only 10% of the maximum capacity. I wouldn't want to judge without trying, though.

Education and experience taught me to always use the proper type and size of equipment. It's faster, cheaper, and gives higher yields. I you have a large column that costs thousands, you can sure afford an additional smaller one at a tenth of the price, can't you?