What you say is basically true, and it applies most to longer and slower pieces, from doxologies, to doxastika, to polyeleoi and psalms, polychronia, and such. For the most part, in terms of adherence to the original prosomoia and automela, they do a fair job (although, e.g., Malek's triodion pieces, including pieces such as Meth imwn o Theos and Kyrie twn dynamewn are heavily orientalized).
But the basic problem is that they (Murr included) don't see that composing pieces in makams is simply not part of the tradition, regardless what Pringos and Stanitsas have done. And yet, if you look at Malek's psalms, they are almost all composed in makams (which he regularly identifies at the top of the piece: nihavent, kurdi, hicazkar, acem, sabah etc.). You can hear examples of that here. Psalm 8:
http://www.youtube.com/watch?v=lMn3HL4fJ-4
Psalm 29:
http://www.youtube.com/watch?v=Qho388Aaibk
This is deeply related to the held belief that there is a basic identity between the 8 modes and their "counterparts" in Ottoman makams (which they refer to as "Arabic music"). And so, liberties are taken in composition and phraseology. This is a politico-ideological issue as well that has become intertwined with a constructed Arab nationalist identity that they feel they must assert (vis a vis Greek), and in many ways is an extension of what Murr was doing early on (aside from church music, he composed nationalist hymns). It's a long, convoluted and ultimately pitiful story, where much ignorance is at play.
Furthermore, many psaltai are trained or go on to study classical Ottoman ("Arabic") music. George Abu Haidar of SEM and the Mt. Lebanon choir, for instance, is a good example. There are several others in the SEM choir who also do this. Fr. Malek himself has a background in this music and is an Oud player.
The issue of orthography is another issue, and I simply don't know what references are consulted. I know Greek theory books are readily available (there's a lot of travel back and forth to Greece) and have been consulted. I also know that there is awareness of certain orthographic rules, though how pervasive and thorough that awareness is, I don't know.
In many ways, that was the point of SEM's mission statement: to adhere more closely to original Greek formulaic lines and to contest the premise that the Arabic language cannot be 100% adapted to these lines. They set out to prove -- with considerable success -- that you can in fact chant in Arabic while adhering to the Greek musical lines. Hence the point of their concert with Idimelon, where the latter would chant a line in Greek and SEM one in Arabic of the same composition.
http://www.semlebanon.org/sem/showClip.do?id=13&menu=1
Another issue has been that the texts themselves were often translated to Arabic without a proper appreciation of their poetic nature in Greek, which is directly related to the prosomoia, for instance. So there is no poetic counterpart to the Greek in the current textbooks (menaion, octoechos, etc.) even as these books state the model automelon for each piece.
All these issues therefore require that a thorough overhaul of the existing texts, and the music books based on them. A massive project, that is.
You can get an idea of a Yazbeck composition here, in the item I am attaching. Again, the mixing of modes is itself testament to what we are talking about, despite a fairly serious knowledge of the music itself.
On a separate note, those who want to hear the troparion of Kassiani as it is found in Murr's book, you can see the choir led by Fr. Romanos Jibran perform it here:
http://www.youtube.com/watch?v=xNfm5u3Is2c
Compare it with Symonidis, who about two thirds of the way into this recording, can be heard chanting the Arabic version:
http://www.analogion.com/EliasElRoomi/EliasElRoomi-I_en_Pollais_Greek.mp3