I'm actually still not so sure because I looked at the two links that you sent at the very top here, and I don't really see an alignment issue. Maybe you're understanding it differently than how it works.
See, for example, if you have a frame at the top of 12% and you have a Browser Height row underneath.
Then the height of the whole layout is:
12 % Top Frame + browserheight Row
In actuality, it's larger than a browser height.
If you want a Browser Height section and in there things should have space to the top, for example, then you should just set frame-top to 0.
And then just click some element that is within the row at the top, and then change its space-top or inner-space-top value in the sidebar.
But as I said, I'm still not sure if that's even what you mean, so if you could elaborate further, that would be great, or maybe send the right screenshots.