xsl:apply-imports to a variable?

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A.xsl imports B.xsl, which contains a function used in A.xsl. A.xsl contains the identity template. B.xsl's function needs to apply template rules to a variable; however, the identity template in A.xsl is overriding them.

My thought was to xsl:apply-imports to the variable in B, but unlike xsl:apply-templates there is no way to select= to point it to a variable. The original functions can't be replaced with template rules. Is there a way to do this without xsl:include-ing B.xsl?

A.xsl:

<xsl:stylesheet 
    xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
    xmlns:xs="http://www.w3.org/2001/XMLSchema"
    xmlns:my="http://me"
    version="2.0">

    <xsl:import href="B.xsl"/>

    <xsl:template match="X">
        <xsl:sequence select="my:do-stuff(.)"/>
    </xsl:template>

    <xsl:template match="@*|node()" mode="#all" priority="-1">
        <xsl:copy>
            <xsl:apply-templates select="@*|node()" mode="#current"/>
        </xsl:copy>
    </xsl:template>

</xsl:stylesheet>

B.xsl:

<xsl:stylesheet 
    xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
    xmlns:xs="http://www.w3.org/2001/XMLSchema"
    xmlns:my="http://me"
    version="2.0">

    <xsl:template match="X" mode="cleanup">
        <clean><xsl:apply-templates/></clean>
    </xsl:template>

    <xsl:function name="my:do-other-stuff">
        <xsl:param name="x" as="element(X)"/>
        ...
    </xsl:function>

    <xsl:function name="my:do-stuff">
        <xsl:param name="x" as="element(X)"/>            
        <xsl:variable name="x-updated" select="my:do-other-stuff($x)"/>
        <xsl:apply-templates select="$x-updated" mode="cleanup"/>
    </xsl:function>

</xsl:stylesheet>
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One option is to prevent the identity template from overriding by changing mode="#all" to list all modes except cleanup:

<xsl:template match="@*|node()" mode="#default not-cleanup1 not-cleanup2" priority="-1">
    <xsl:copy>
        <xsl:apply-templates select="@*|node()" mode="#current"/>
    </xsl:copy>
</xsl:template>