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Smith - Formless Spawn, Shoggoth? — Description
Okay, for some reason the Formless Spawn by many is believed to be a different type of creature than a Shoggoth. This statement, in my opinion, is wrong. Amorphous blobs of black goo that form temporary limbs are already present within the Mythos universe and I think it is baseless to assume there are two different types of creatures that fit almost identical description especially as the two writers have many times shared each other's concepts in their work.

Small differences between the two, I think might come from the environment they lived in. Antarctic Shoggoths were very much active creatures and had plenty of food didn't need to conserve energy. Therefore creating multiple temporary eyes on their surface seemed an agreeable deal. Formless Spawn, on the other hand, works as a temple guardian. It is dormant most of the time and only feeds on desecrators if there are any. In such circumstances, the creature would naturally aim to conserve as much energy as possible and not waste it on creating temporary, "expensive" organs such as eyes.
Their legs and mouth are also an interesting case. I believe it is due to the Shoggoth/Spawn "learning" anatomy of its handlers. The shoggoths have obviously copied vocal organs of the Elder Things as they could mimic their sounds. It is also natural that they had multiple tentacles, just as Elder Things did. I think it's believable that the Shoggoth being trained/cared/commanded by a human being would learn to copy some of the vertebrate characteristics such as legs and mouth.

"Then two arms—if one could call them arms—likewise arose inch by inch, and we saw that the thing was not, as we had thought, a creature immersed in the liquid, but that the liquid itself had put forth this hideous neck and head, and was now forming these damnable arms, that groped toward us with tentacle-like appendages in lieu of claws or hands!"

Clark Ashton Smith, The Tale Of Satampra Zeiros