You are right, there is a "double coverage". The EUPL just states that the compatible license (applied to the combined derivative work) will prevail in case it conflicts with the EUPL. But none of the listed compatible licenses (i.e. GPL-v2 or GPL-v3) prohibit, for example, the coverage of remote/SaaS distribution: they may not impose it (SaaS loophole) but allow it. So the EUPL code inside the combined derivative will stay covered by essential EUPL obligations, including the modified code sharing in case of remote distribution, even when the combined work is globally distributed under the GPL.