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It is and isn't controlled when a change in their appearance happens, just as it is in humans. They just can have bigger differences in their appearance than hair growing a few millimetres or wrinkles forming on their skin, or a change of clothes and make up if they wanted to focus on appearance shifts that humans made. Sometimes Will wondered why humans never acknowledged their own shapeshifting, instead ignoring it because in the biggest difference to their own, their shifts were mostly painless.
The ones their family go through are never painless, even if they don't intend to change and the pain is their alert that it's happening. Constantly having to reverse the bigger ones made it all worse as well, because their bodies weren't meant to be fixed, but as their mum said, to remain safe they couldn't shift constantly.
It made being lost to the Upside Down almost a relief as Will could let go of that mindset, and accept their bodies shifting as both they wished for it to, and it would be doing regardless. The shifting was even helping them improve their ability to fight back and survive and they for the first time could carry on without constantly thrumming in pain left over from forcing themself back into an old form.
The changes are enough that Hopper doesn't recognise them when he comes with their mum to rescue them. Will actually laughs when they see the gun pointed at them, waving to their mum for a moment before being swept into a hug. They then can relax as she guides their powers slowly, quietly back into their recognised shape. At least being guided by another shapeshifter means less pain but her and Hoppers mentions of the doctors waiting for them are chilling. Avoiding shifting entirely was a requirement when in hospitals, one they always struggled with. They knew it would be harder after this time experiencing what it's like to let the shifts happen freely.