Scaling an SVG

I don’t really understand what you are trying to do.
But if it is to scale the rectangle then either enclose it in a svg tag and set the origin and dimensions of that svg tag like this

<svg xmlns="http://www.w3.org/2000/svg">
    <filter id="filter">
        <feTurbulence baseFrequency="0.01 0.0001" numOctaves="5"/>
        <feColorMatrix values="1 0 0 0 0
                               0 0 0 0 0
                               0 0 0 0 0
                               0 0 0 0 1"/>
    </filter>
    <svg x="25%" y="25%" width="50%" height="50%">
      <rect width="100%" height="100%" filter="url(#filter)"></rect>
    </svg>
    
</svg>

Or set the origin and dimensions of the rectangle.