Sorry had to leave last night....
I never really even looked at the spacer templates before but it looks like they set the width and padding of the style between the header and footer based on the values in your StyleVars and also checks if you are running a very old version of IE.
Hopefully someone can give you a more definitive answer.
HTML Code:
<if condition="$show['old_explorer']">
<table cellpadding="0" cellspacing="0" border="0" width="$stylevar[outertablewidth]" align="center"><tr><td class="page" style="padding:0px $stylevar[spacersize]px 0px $stylevar[spacersize]px">
<else />
<div align="center">
<div class="page" style="width:$stylevar[outerdivwidth]; text-align:$stylevar[left]">
<div style="padding:0px $stylevar[spacersize]px 0px $stylevar[spacersize]px" align="$stylevar[left]">
</if>