I'm sorry, but your response doesn't seem to me to argue a position. Being close to zero is saying that its 'small' with different words, and as I don't understand what the problem is with having small numbers, neither do I understand the problem with having numbers that are close to zero...
I want to convince you that small numbers, close to zero, on some scale, are not inherently problematic. I would like you to try to convince me that they are, or that at least you have a special case in which they are are a problem given your context.
5e-06 meters is 5000 nano-meters.
is 5000 close to zero ?