I don't think it matters within reason- the "cover" only acts to hold the choke outer cable statianary when the lever is activated, thus pulling the inner "in" and activating the choke mechanism.
"Within reason" means that a cable stay that is not fitted well will alter the ratio between the inner and outer cables. This may affect your ability to adjust the choke mechanism. You may not be able to turn it off.
My cable stay slips over the choke lever beyond the two slits in the cable stay. You can always file down the outside of the barrel of the lever so that the sleeve slips over to a correct depth.