This is a good point. Charlotte and Felix married on 6 November 1919, not quite a year after the Armistice, when memories of the German occupation must have been absolutely raw.
A quick check of wikipedia shows that the two were first cousins through their mothers, who were both daughters of King Miguel I of Portugal, but (naughty thought here!) two of Felix's numerous brothers, Xavier and Sixtus, had served in the Belgian Army in WW1, which would have made them much less controversial candidates! Sixtus married in March 1919 but Xavier did not marry until 1927. Another brother, Rene, also served in the Austrian Army. Perhaps Charlotte just preferred Felix, despite the complications!
Ann