When starting mongos with a specific value for the --chunkSize parameter this parameter will be ignored if there's already a chunkSize setting in config.settings. This basically means there's no officially supported way to change the chunkSize setting. I can certainly think of a few cases where MongoDB shouldn't allow this value to be modified but there are some valid use cases.
Would it be possible to always respect the --chunkSize setting and error out if the setting is invalid for whatever reason? Or even better add an admin command for it. I've already run into a number of cases where I'd like different chunksizes for different collections for example so an additional (optional) parameter to the "shardCollection" command might be a good route to take.