The text in the PowerFrameworks template will assume the default setting for text in your template. This is a good thing and a bad thing all at the same time. You want the font to change to your template's default font as well as the sizing and attributes (bold, italic, etc.) - this is the good part. The bad part is that there is some extra formatting that needs to take place to get it to look okay again. For example, your 24-point default font size may not be correct when labeling an axis.
Unfortunately, there is not way to make a series of charts vanilla enough to blend with every template out there. Importing the PowerFrameworks charts is still preferred over the default charts in PowerPoint. Many of the default charts in PowerPoint have both the segment value and an axis, which is redundant and should be avoided. See the FAQ on values and axes.