As PhoneDr referred to, the article is only saying that 128Gb version would be added. If I were to speculate, my guess is that the present form of the SE will stay as it is. The only refresh is storage upgrade, which does not change anything else. There appears to be 3 sizes/classes of iPhone coming this year, which includes 4.7 inch, bezel change or not. On top of it, Apple seems so eager to start assembling SE in India, which indicates to me that SE stays in its current package for foreseeable future. It would be nice to have a 4 inch size iPhone with bezel-less 4.7 inch with A10 chip etc. OTOH, I cannot see any reason that Apple suddenly drops SE. Addition of 128Gb storage size might be the indication that Apple continue to sell it in the 1st world market.
So if you look at the line up of SE, 7, and 7Plus from a screen dimension it's very interesting. You can almost lay the devices over each other. Examples:
Lay the SE on top of the 7. If you went all screen edge to edge with the SE and no bezel the screen size would be the same as the 7.
Here's were it gets super interning and rumor mill starts. Lay a 7 on top of a 7Plus. The 7 fits exactly and lines up to the screen dimensions on the Plus. The if you removed the bezel from 4.7" iPhone and went all screen edge to edge you'd have the screen real estate of a Plus.
Think about that, if an iPhone 7 had no bezel, the screen would be as big as the Plus. So think about what that would mean for a Plus with no Bezel.
Then there is the "middle" rumored device. A 4.7" standard, a Plus, and 5" inch all glass front back with all the bells and whistles.
Appears that there will be something for everyone and everyone can count on innovation is some way which the 6s and 6s Plus IMO lacked against the 7 and 7 Plus. I really like my personal 7 but my work 6s works flawlessly.