Well, it used to be true that fop did not support the xsl-footnote-separator
static content in a page master, and it is still not listed in their
supported elements. However, it appears to work now, so I guess the
stylesheet should be updated.
In the mean time, you can customize the setup.pagemasters template in
fo/pagesetup.xsl by moving the call to the footnote-separator template to
outside the if statement:
<xsl:if test="$fop.extensions = 0">
<xsl:call-template name="blank.page.content"/>
</xsl:if>
<xsl:call-template name="footnote-separator"/>