It's perfectly safe, in fact that's what you're supposed to do when a battery is too small. I always charge my 14500 and LiMn 16340 together in the WF-139 charger, which includes a couple of ball bearing spacers so the 16340 will fit.
It's 4 channel. I was thinking how safe is it to use a bit of metal to charge a 16340 when the charge accommodates a minimum cell length of 50 mm. is the charger going to be too hard on the smaller battery?