Belly buttons are scar tissue, an indentation (innie) or protrustion (outie), made where the umbilical cord broke away from the abdomen. The size and shape of a belly button has nothing to do with clamping, tying, cutting or not - it is what it is. It is not genetic and you can't blame the midwife.
To make a little button for your baby doll you will need a small piece of scrap body fabric a couple of inches long and less than an inch wide, sharp scissors and a needle and thread. You doll should be stuffed but preferably without its head yet on (Tho I have done it when the doll is complete, it can be a bit fiddlier tis all).
Along the long side, fold the fabric into thirds and begin whip stitching the sides so that it kind of makes a flat tube.
When you have stitched about an inch, roll (scroll) the tube so your stitches are on the inside and whip stitch the bottom to hold it in place.
Keep rolling and stitching til you get it the size and shape you want then snip off the excess fabric on a diagonal and carefull fold in the raw edges and neatly stitch in place.
Then try it on for size and pick your position.
To start with, secure your spot on the abdomen with a couple of stitches (I don't cut my threads between the making of and the placing on so it is pretty secure) and then secure the belly button by working around in ladder stitch three or four times.
First through the lower edge of the button
and then through the skin of the abdomen.
You can be sure that inquisitive fingers will pull at and play with the belly button so be sure it is on tight! To finish I like to pull it and make a bit of an indent. To do that I come up through the center of the button and then back down into the abdomen stuffing. Now depending on the length of your thread and your preference you can either come down and out somewhere in the groin or up through the neck hole - either way make sure you catch plenty of stuffing and then turn around and go back where you came out and back into the belly button.
Tie it off really securely, make three knots, and then bury your thread into the body somewhere before snipping off.
She doesn't look so cute headless, and armless but I tell you she has a VERY cute bottom!