Finally, taking ideas from you and modifying it a little bit, here is what I got.
Original XML:
<Reporte>
    <idoperacion>10</idoperacion>
    <Operacion>
        <Tipo>Lavado</Tipo>
        <Fecha>01/02/2018</Fecha>
    </Operacion>
    <Persona_Fisica>
        <Nombre>Juan</Nombre>
        <Apellido>Perez</Apellido>
        <Domicilio>
            <Calle>Falsa</Calle>
            <Nro>123</Nro>
        </Domicilio>
    </Persona_Fisica>
    <Persona_Juridica>
        <Denominacion>Lavado SRL</Denominacion>
    </Persona_Juridica>
    <Persona_Fisica>
        <Nombre>Jose</Nombre>
        <Apellido>Lopez</Apellido>
        <Tipo_Documento>CUIT</Tipo_Documento>
        <Nro_Documento>12345678</Nro_Documento>
        <Domicilio>
            <Calle>Sarasa</Calle>
            <Nro>1234</Nro>
        </Domicilio>
        <Telefono>
            <Numero>1234-5678</Numero>
        </Telefono>
    </Persona_Fisica>
</Reporte>
XSLT:
<?xml version="1.0"?>
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
    <!-- Object or Element Property-->
    <xsl:template match="*">
            <xsl:text disable-output-escaping="yes"><</xsl:text>
            <xsl:value-of select="name()"/>
            <xsl:text disable-output-escaping="yes">></xsl:text>
            <xsl:call-template name="Properties"/>
            <xsl:text disable-output-escaping="yes"><</xsl:text>/<xsl:value-of select="name()"/>
            <xsl:text disable-output-escaping="yes">></xsl:text>
    </xsl:template>
    <!-- Object Properties -->
    <xsl:template name="Properties">
        <xsl:variable name="childName" select="name(*[1])"/>
        <xsl:choose>
            <xsl:when test="not(*|@*)"><xsl:value-of select="."/></xsl:when>
            <xsl:when test="count(*[name()=$childName]) > 1"><xsl:value-of select="$childName"/>[<xsl:apply-templates select="*" mode="ArrayElement"/>]</xsl:when>
            <xsl:otherwise>
                <xsl:apply-templates select="@*"/>
                <xsl:apply-templates select="*"/>
            </xsl:otherwise>
        </xsl:choose>
    </xsl:template>
    <!--ID Reporte-->
    <xsl:template match="idoperacion">
         <id><xsl:value-of select="."/></id>
    </xsl:template>
    <!--ID-->
    <xsl:template match="Operacion | Juzgado | Causa_Penal | Delito | Inmueble | Automotor | Producto | Persona_Fisica | Telefono | Domicilio | Persona_Juridica">
        <xsl:copy>
            <id><xsl:value-of select="ancestor::Reporte/idoperacion"/><xsl:text>.</xsl:text><xsl:number level="multiple" count="*" from="Reporte"/></id>
            <xsl:apply-templates/>
        </xsl:copy>
    </xsl:template>
</xsl:stylesheet>
New XML:
<Reporte><id>10</id>
<Operacion>
   <id>10.2</id>
        <Tipo>Lavado</Tipo>
        <Fecha>01/02/2018</Fecha>
    </Operacion>
<Persona_Fisica>
   <id>10.3</id>
        <Nombre>Juan</Nombre>
        <Apellido>Perez</Apellido>
        <Domicilio>
      <id>10.3.3</id>
            <Calle>Falsa</Calle>
            <Nro>123</Nro>
        </Domicilio>
    </Persona_Fisica>
<Persona_Juridica>
   <id>10.4</id>
        <Denominacion>Lavado SRL</Denominacion>
    </Persona_Juridica>
<Persona_Fisica>
   <id>10.5</id>
        <Nombre>Jose</Nombre>
        <Apellido>Lopez</Apellido>
        <Tipo_Documento>CUIT</Tipo_Documento>
        <Nro_Documento>12345678</Nro_Documento>
        <Domicilio>
      <id>10.5.5</id>
            <Calle>Sarasa</Calle>
            <Nro>1234</Nro>
        </Domicilio>
        <Telefono>
      <id>10.5.6</id>
            <Numero>1234-5678</Numero>
        </Telefono>
    </Persona_Fisica></Reporte>
This has some obvious bugs:
- Indentation: it's clear it's not indenting properly, but it's not so
important at this point.
 
- ID sequence: it's considering initial ID as
the first element, so the second ID is "original_id.2" instead of
"original_id.1". Also, it doesn't restart sequence properly when
adding a new element (for example, 10.5.5 goes after 10.5 instead of
10.1). However, it accomplishes the goal of a hierarchical ID (all numbers are different and you can determine which elements are
father and son).
 
Thanks all for your help!