First of all the "lengthening" of the ship (by 16 meters) ain't much of an argument. You can change the length of a Starfleet starship simply by replacing its nacelles and/or nacelle pylons. On paper the ship will change it's length without the actual body of the ship having been shortened or lengthened.
Secondly and more importantly, you're missing the point. The point isn't that the refits being done to the Midway are exactly like the ones done to the Enterprise. And how could they? One is a 20th century aircraft carrier and the other is a fictional 23rd century starship.
Oh now, this is not what was done, not at all. Lets look at the ships, side by side.

First off, no one would ever honestly claim this is the same class of ships. I did a fast and dirty size here based off pixals of the image. The "refit" does have longer nacelles, which is to be expected. But lets walk though everything.
- The TOS Secondary hull is only 404 px long and 104 tall, the TMP is 431 long and 113 px tall. The shape is clearly not the same.
- The whole deflector assemblage is in a whole other place. Its much deeper on the TMP design.
- The Tos Saucer is 486 px long by 125 tall. The TMP version is 560 long and 231 tall. It not the same saucer, it is both taller and a good bit longer and wider.
- The Nacelle pylons have moved! not just the shape but the very location, which would mean a massive rework of bracing.
- The neck designs are the closest thing the two share and even they are not alike.
- the total height without nacelles is 255 px vs 273.
- The total length without nacelles is 783 px vs 866 px.