1.4" and 1.6" are nominal sizes. They don't indicate the actual rim width. It's dumb, I don't know why Honda did it but they did.
Grab a measuring tape and measure the rims for yourself. You'll find the front is actually about 2.1" wide and the rear is actually about 2.3" wide (reference: http://www.dontai.com/cb125s.htm, see the section about tires).
3.00" is the nominal tire width. Again, nominal doesn't mean actual width. Here's a good write of tire sizes explained: http://www.revzilla.com/motorcycle-tires-101-guide
Also, in the manual it calls for a 2.75" x 18" tire for the front and a 3.00" x 17" tire for the rear. Here's a screenshot I took of the CB125S shop manual (there's a copy of it floating around on DTT somewhere
): http://i.imgur.com/RE7AIXh.png
As much as I hate Motorcycle Superstore, they have the SR241 in a 2.75" x 18", and a 3.00" x 17":
http://www.motorcycle-superstore.com/18730/i/shinko-sr241-front-rear-dual-sport-tire
They also have the 244 in a 3.00" x 18" front and a 3.00" x 17" rear:
http://www.motorcycle-superstore.com/15034/i/shinko-244-dual-sport-front---rear-tire
If you're worried about clearances, ask yourself if there's an extra 1/4" for the tire to occupy between the forks.