From the XSLT spec, it looks like imported templates always have lower precedence than conflicting templates with higher import precedence (where the main XSLT would have the highest import precedence), but perhaps this is a suitable workaround?:
<xsl:stylesheet version="2.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
<xsl:template match="/">
<xsl:element name="cow">
<apply-templates select="." mode="regular">
</xsl:element>
</xsl:template>
</xsl:stylesheet>
<xsl:stylesheet version="2.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
<xsl:import href="cow-wrapper.xsl" />
<xsl:template match="/" mode="regular">
<!-- regular stuff to do -->
</xsl:template>
</xsl:stylesheet>