From what I see placeholders seem to ignore the height anyway and the content isn't constrained in the y direction which is good. The placeholder only seems to be constrained in the width but in most cases I'd imagine defining the position and width is ideal.
I don't think the problem is with placeholders but with how the whole of the content/page reacts to dynamic content displayed by placeholders.
The reason I would add scrollbars to placeholders is because the rest of the page content doesn't move to accommodate the dynamic content in placeholders. If you've got a placeholder positioned above anything (in y dir) it's going to overlap what's below it because the content below doesn't move down. If you do use the javascript tweak it ties it to the footer and leaves unwanted gaps.
Ok this bit might be getting a few steps ahead but also if you use something like an accordian menu or something that expands/shrinks it gets even more complicated for a javascript solution to deal with, which is why a html/css solution would be better and more accommodating than a javascript one which just won't cope in as many scenarios.
See image attached...
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