AFAIK the only output of DNA transcription are proteins but how are things like skeletal structure encoded? I mean things that are not functional specialization like the shape of my nose or the size of my forehead or the length of my legs.
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Basically the cells in your body are like little factories that build stuff. However, they also have “antenna” on the outside to pick up signals from the surrounding cells/outside the cell. Some of these signals will tell you cells to do all sorts of stuff (stop, go, go faster, die, etc). The cells themselves can also make these signals, it’s a whole network (like, your entire body’s billions of cells). Anyway, some things like bones will basically stop growing once the cells in a certain part of the bone receives enough “stop” signals.
There’s been lots of developmental biology experiments performed to basically see, “Hey, what happens if we turn this gene on so that it never stops?? Or what if we turn it off completely? What if we gave them extra copies?!” For example, many cats have extra toes because of a mutation in a gene called sonic hedgehog, which plays a role in limb patterning (like how your fingers and toes are organized). When the gene is expressed when it’s not supposed to be, this signal tells the cells to create an entirely new toe, so then your cat ends up with more toes.
While having an extra toe is mostly harmless, but things can go totally, horrifically wrong depending on what signals get released when they shouldn’t have been (or conversely, when there should’ve been a signal but it wasn’t there). Cyclopia is a birth defect where the fetus most notably has 1 eye. The same gene we just talked about (sonic hedgehog) is also responsible for this. If not expressed properly, the eye doesn’t get the signals required up divide into two, so you just get this mega eye in the middle.
TL;DR: cells talk to each other. Usually works out, sometimes miscommunication happens.
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