No, the whitespace removal works like a charm, as far as I could test it for now.
What I ment was that when you don't do anything with the SVG the SVG just renders correctly even with the extra white spaces and new lines.
When you apply a tween to it like animate from 0 to 100% then the start/end points get shifted like in the first example.
We've build something similar before the SVGplugin existed with only paths and using the getTotalLength method. The behaviour the original SVG now gave with the plugin looked similar to when the getTotalLength method for paths gave a wrong value (like sometimes happens in Firefox) that's why I assumed the polylines use something similar.
Since the plugin makes life a lot easier we decided to migrate our code.
This is a snippet of what I've used before using the plugin to set all the paths before animating them.
var paths = document.querySelectorAll('path');
for (var i = 0, l = paths.length; i < l; i++) {
var path = paths[i];
var pl = path.getTotalLength();
path.setAttribute('data-pathlength', pl);
TweenMax.set(path, {strokeDashoffset: pl, strokeDasharray: pl + " " + pl });
};