"Elative" can mean either the comparative and the superlative in semitic languages, but the superlative is suitable here, since the equivalent in the Second World War was "Most Secret". I would use Plej Sekreta for this reason.

Chainy:

noelekim:

Miland:How about "Unclassified"? "Commercial-in-confidence"? "NOFORN"?

NOFORN (not for distribution to non-U.S. citizens) - distribuo restriktita al usonaj civitanoj

I wonder what the point of 'restrikt/' is, when we have 'lim/ig/i'? Or can you think of some cases where the latter might not fit?

I looked for examples of 'restrikti'/'restrikto' in our literature (see below) and I couldn't find one where 'limigi'/'limigo' wouldn't do as well. So 'restrikti' is a synonym.

If you are asking, what is the point of synonyms, I think they enrich a language.

Examples:
Oni do povas kompletigi la ĉi-supran uzregulon de la refleksivo per jena *restrikto*: Preferinde ne uzu la refleksivon, se ...
Plena analiza gramatiko de Esperanto - 1985 - http://goo.gl/KbGBY

RESTRIKTO: formo de nerekta prezregado sur la mondmerkato fare de produktistoj
International business dictionary in eleven languages - 1990 - http://goo.gl/eO15D

... lia eksterna ekzistado preskaŭ komplete *restriktis* sin al la belega urbo kiu fariĝis lia hejmo,
La Morto en Venecio, tradukita de Petro Buijnsters - 2006 - http://goo.gl/vHXGS

Preskaŭ la tuta homa historio estas padodependa, en la senco ke jam faritaj decidoj, ne plu pravigeblaj, *restriktas* la aron de nunaj opcioj ...
Ken Miner. Beletra Almanako 8 - 2010 - http://goo.gl/0Mbr1

Is there a real difference in meaning? And even if there is, does the presence of the "incorrect" parsing make the "correct" one unusable?

You only have to consider the meaning of sekreteto to bring out the meaning of sekretego.

A 'little secret' is one whose public exposure is not of great consequence, the reverse situation applying to a great secret. A little secret is not one whose secrecy is reduced or restricted.

If I remember my John le Carré correctly it was Karla the Russian spymaster who was suspected by Smiley of harbouring a great secret (sekretego).

In the case of 'sekretega' the two analyses are not comparable to the two analyses of, say, 'kolego', which depend on whether this is composed of two elements or three.

The ambiguity in sekretega, sekret(o)ega and sektret(a)ega, arises because 'sekret' is one of those roots where the noun and adjective usages are both ordinary. Unlike say 'bus' where buso predominates over busa, leading to busega having only one plausible interpretation, ie pertaining to a monster bus, not monstrously bus-like.

'Plej sekreta' certainly deserves consideration. But to say that something is plej sekreta is not necessarily to give it the grade of being 'la plej sekreta', which I assume is what 'top secret' means, although outside the security domain that term is somewhat debased.