As Ankh said, all readers have to define a base size for fonts, and your base font definition will use that, so setting it to 1em or 100% will simply use the default base size.
An important thing to remember is that while all readers will allow the font size to be increased, few (if any) allow it to be decreased, so the base font size is the minimum size that will be used. On my Sony 505, text at 100% renders at a height of 2.1mm, which is approximately 6pt. This size should be clearly legible to anyone with good eyesight and it provides a line measure of around 56 characters, which is close enough to the ideal of 66.
Increasing the base font size will produce clearer and better-rendered characters, at the expense of having fewer per line and less text on the page. This is a decision that's best left to the reader.