It seems that the context should not be the best for this use of « en … pas moins », that is the author used this form when he/she might have done better to use something else, as I see it; to expand a little on what I am saying I’d say that it is not at all obvious that because a question is legitimate and necessary it should also not raise a problem and be difficult. Although this is not a form I can find in the dictionary it is fairly familiar to me, but I find it in contexts that seem more appropriate; here is an example of use I think irreproachable.

• Tout puissant qu’il soit, il n’en est pas moins sans ressources contre de simples moustiques.

« en » refers to the power ; what is then said is a remark on what one would think could result from that power but which, surprisingly enough, doesn’t: nevertheless, irrespectively of all that strength, he is vulnerable if attacked by simple mosquitoes.

The two words are used together as far as I can remenber. However, there is a way do use something else instead of “moins”; the construct is changed slightly.

• Tout puissant qu’il soit, il n’en est pas plus protégé contre de simples moustiques.

This inversion shows that “moins” is not a redundant word in the sentence.

“Moins” is not redundant, removing it would reverse the meaning of the sentence:

• “ne soulève pas” means “doesn’t raise”

while

• “ne soulève pas moins” means “nevertheless raise”.

“En” refer to “légitime et nécessaire“, i.e. “ne soulève pas moins du fait qu’elle soit légitime et nécessaire…“

The sentence might be simplified this way:

Bien que légitime et nécessaire, cette question soulève immédiatement une difficulté qui semble insurmontable.

Insoluble questions are often little appreciated but the context should better explain why the author put in opposition “legitimate and necessary” and “insurmountable”. Here is a guess about what (s)he had in mind:

Bien que la question s’impose (et mériterait d’avoir une réponse satisfaisante), elle semble cependant insoluble (et voici pourquoi on ne sait pas y répondre…).

Note that “pour … que” is used in a rare, literary way to introduce a concessive clause (similar to even though or despite in English), like this excerpt from the TLFi pour entry shows:

C.− [Marque l’idée de concession]
…
2. Pour + adj. + que (+ subj.). Il (…) lui jura que, pour grand que fût son amour, son amitié l’emportait de beaucoup encore (Gide, Caves, 1914, p. 763). Ce succès, pour modeste et incomplet qu’il fût, m’apparaissait comme une première étape vers la victoire (Joffre, Mém., t. 2, 1931, p. 61). Je me sentais perdu et, pour absurde que cela paraisse, j’eus un bref mouvement de désespoir (Bosco, Mas Théot., 1945, p. 108).