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.