Here is article 227 of the Pakistani constitution:
227. Provisions relating to the Holy Qur’an and Sunnah.
(1) All existing laws shall be brought in conformity with the Injunctions of Islam as laid down in the Holy Quran and Sunnah, in this Part referred to as the Injunctions of Islam, and no law shall be enacted which is repugnant to such Injunctions.
 [Explanation:- In the application of this clause to the personal law of any Muslim sect, the expression “Quran and Sunnah” shall mean the Quran and Sunnah as interpreted by that sect.]
(2) Effect shall be given to the provisions of clause (1) only in the manner provided in this Part.
(3) Nothing in this Part shall affect the personal laws of non- Muslim citizens or their status as citizens.
The “Part” referred to in Article 227(2) is Part IX of the constitution . Part IX describes the procedure for the Council of Islamic Ideology to decide whether or not a proposed law is repugnant to the injunctions of Islam. Part IX does not describe the manner in which any other institution could go about deciding a law is repugnant to the injunctions of Islam via article 227(1). So what article 227(2) does is limit the scope of article 227(1) to the Council of Islamic Ideology.
In the NRO verdict short order, article 227 is mentioned as follows:
(i) that the NRO is declared to be an instrument void ab initio being ultra vires and violative of various constitutional provisions including Article Nos. 4, 8, 25, 62(f), 63(i)(p), 89, 175 and 227 of the Constitution;
Since the Supreme Court bench is not the Council of Islamic Ideology, this is going against article 227(2).
As pointed out by Monsoon Frog:
However, the same article also provides that clause (1) of Article 227 shall only be given effect through referral of a matter to the Council of Islamic Ideology, which in turn is only empowered to give an advisory opinion.
So to my non-lawyerly mind it seems rather clear that the short order has essentially widened the scope of Article 227(1) beyond its constitutional limits as described in Article 227(2).
The position as far as a lay writer can understand is this: the power to strike down a law for being repugnant to Islamic injunctions lies with the Federal Shariat Court and no other court. Article 227 only allows the Council of Islamic Ideology to recommend changes in laws on the ground of repugnancy to Islam. The article does not empower any forum to strike down any law. When 17 judges of the highest court invest Article 227 with the power to nullify a law it could amount to constitution-making.
I am grateful to the two writers above for clarifying this aspect of the short order. As far as I can tell they appear to be the only two legal experts who have described this contradiction and its troubling implications. Babar Sattar, in his column, while discussing the mention of article 227 in the short order, omits any mention of article 227(2).
It’s interesting and sad that an aspect of the short order with such potentially far-reaching consequences regarding the future use of the Islamic provisions of the constitution by our courts has gone relatively undiscussed in both the Pakistani and the foreign press.