Hola de nuevo.
Después de varios días y tiempo investigando y probando creo que una opción temporal (o quizás única) podría ser poner siempre en el código html debajo la provincia que se tapa, por ejemplo en este casi pondría Vizcaya encima de Guipúzcoa y listo. Luego si a la vez esta se superpone con otra o roza moviendo las coordenadas x e y pues la desplazo para que no se superpongan y así con eso por ahora creo que me puede servir.
Ejemplo: Pongo arriba Vizcaya, muevo el texto en x un poco mas a la izquierda x="308.99408", debajo la que no se veía y listo.
Código HTML:
Ver original<svg id="svg3609" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.1" class="map-svg">
<!-- Vizcaya -->
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<text id="text757" transform="scale(.99995 1)" y="26.83588" x="308.99408"> <tspan id="tspan759">Vizcaya</tspan>
<!-- Guipúzcoa -->
<a class="%current49%" id="guipuzcoa_map" xlink:href="%judet49%"> <path id="path16" d="m474.23 42.243v0.24002h-0.24-0.23999-0.24v0.24001-0.24001l-0.23999 0.24001h-0.24-0.47998v0.24002l-0.24 0.24002v0.24001 0.24002 0.24002 0.24001 0.24002h-0.23999v0.24002h-0.24-0.23999v0.24001l-0.24 0.24002h-0.23999v0.24002-0.24002l-0.24 0.24002h-0.23999v-0.24002 0.24002 0.24001h-0.24 0.24-0.24v0.24002-0.24002h-0.23999v-0.24001-0.24002h-0.23999-0.24 0.24v0.24002h-0.24 0.24v0.24001h-0.24 0.24v0.24002h-0.24v0.24002-0.48004l-0.23999 0.24002h0.23999l-0.23999 0.24002v-0.24002h-0.24l-0.23999-0.24002h0.23999l-0.23999-0.24001v-0.24002l-0.24 0.24002v0.48003l0.24 0.24002-0.24 0.48003-0.23999 0.24001v0.24002l0.23999 0.48003v0.24002 0.24002 0.24001l0.24 0.24002h0.23999v0.24002 0.24001l-0.47999 0.24002v0.24002 0.24001h-0.23999-0.24v0.24002h-0.23999l0.23999 0.24002h-0.23999l-0.23999 0.24001-0.47999 0.24002h-0.24l0.24 0.24002h-0.24v0.24001h-0.23999l-0.24 0.24002v-0.24002l-0.47999 0.24002-0.23999 0.24001v0.24002h-0.23999l0.23999 0.48003v0.24002l-0.47999 0.24002v0.24001l-0.23999 0.24002v0.48003l0.23999 0.48004v0.24001h0.24l-0.24 0.48004-0.23999 0.24001h-0.24v0.24002h-0.95998-0.47998v0.72005l-0.24 0.24001v0.24002l-0.23999 0.24002h-0.24-0.23999-0.24-0.23999-0.24l-0.23999 0.24001h-0.23999-0.24v-0.24001l-0.23999-0.24002-0.24-0.24002-0.23999 0.24002-0.24-0.24002v0.24002 0.24002 0.24001h-0.23999l-0.24 0.24002h-0.23999v0.24002 1.2001l-0.24-0.24002-0.23999 0.24002v-0.24002h-0.47999-0.47999l-0.23999-0.24001v-0.48004l-0.24-0.24001v-0.24002l-0.23999 0.24002-0.24-0.24002h-0.23999l-0.47999-0.24002-0.23999-0.24001v-0.24002h-0.24-0.23999-0.24l-0.23999-0.24002h-0.24-0.23999l-0.23999-0.24001-0.47999 0.24001-0.24-0.24001h-0.23999-0.24l-0.23999 0.24001-0.24-0.24001-0.47998-0.24002h-0.24l-0.47999 0.24002-0.95998-0.48004-0.23999 0.24002 0.23999 0.48003-0.23999 0.24002v-0.24002l-0.23999-0.24001h-0.47999l-0.24-0.24002h-0.23999v-0.24002h-0.24l-0.23999-0.24001v-0.24002h0.23999l-0.23999-0.48003v-0.24002-0.24001h0.23999 0.24l0.71998-0.48004h0.24l0.23999-0.24001v-0.24002l0.23999-0.24002 0.24-0.24001v-0.24002l-0.24-0.48003h-0.23999v-0.48004h-0.23999l0.23999-0.24001v-0.24002-0.24001h0.23999l0.24-0.24002 0.47999 0.24002 0.23999-0.24002v-0.96007h0.24l-0.24-0.72005v-0.48003-0.24002l-0.23999-0.24001v-0.24002h0.23999 0.47999v-0.24002l-0.23999-0.24001 0.23999-0.24002v-0.72005h-0.23999v-0.24001h-0.24v-0.48004l0.24-0.24001v0.24001l0.23999-0.24001 0.24 0.24001h0.47998v-0.24001l0.47999-0.48004 0.24-0.24001v-0.24002l0.47999-0.48003v-0.24002-0.24002h-0.24v-0.24001l-0.47999-0.24002 0.24-0.48003v-0.24002l0.23999-0.24001h0.24v-0.48004h0.23999 0.24l0.71998 0.48004h-0.24 0.24 0.23999l0.24 0.24001h0.23999v0.24002h0.24v-0.24002l0.71998 0.24002h0.23999 0.71999 0.23999 0.24 0.23999v-0.24002 0.24002l0.24-0.24002h0.23999 0.23999v-0.24001h0.47999 0.24l0.23999 0.24001 0.24-0.24001v0.24001l0.23999 0.24002v0.24001l0.24-0.24001 0.23999 0.24001v0.24002l0.71998-0.24002v-0.24001l0.24 0.24001h0.23999 0.24v-0.24001h0.23999l0.24-0.24002 0.71998-0.24001h0.47999v-0.24002h0.71998v-0.24002h0.24 0.47999 0.23999v-0.24001h0.23999v0.24001l0.24 0.24002 0.23999-0.24002-0.23999-0.24001h0.23999 0.24 0.23999v-0.48004h0.24 0.47999v0.24002l0.23999-0.24002h0.23999v0.24002h0.24v-0.24002h-0.24 0.47999l0.24-0.24001 0.47999-0.24002h0.23999l0.24-0.72005 0.23999-0.24002h0.23999v-0.24001h0.24 0.23999v-0.24002h0.47999l0.24-0.24002h0.23999l0.47999-0.24001 0.24 0.24001h-0.24l-0.23999 0.24002v0.24002l0.23999 0.24001v-0.24001 0.24001 0.24002l0.24 0.24002-0.24 0.24001h0.24l0.23999 0.24002 0.23999 0.24002 0.24-0.24002 0.23999 0.24002v0.24001l0.47999 0.24002v0.24002 0.24001 0.24002l0.24 0.48003m-12.48 0.48003" clip-path="url(#SVG_CP_1)" transform="translate(-112.39 -18.688)" fill=""/>
<text id="text769" transform="scale(.99995 1)" y="33.925827" x="327.77164"> <tspan id="tspan771">Guipúzcoa</tspan>
</svg>
No se si habrá otra solución, por ahora creo que esta opción me sirve, aún así lo dejo abierto por si hay alguna otra manera de hacerlo.
Saludos.