Although I have not found other articles to corroborate this, it seems an Asia Times writer was able to talk to a source within the Bangsamoro deal who said,
In an apparent non-disclosed component of the MILF peace deal, Manila agreed to drop its historical claim to territories in Sabah in exchange for the establishment of a Philippine consulate in Sabah, according to a source familiar with the provision. Revelations of the that concession to Malaysia reportedly infuriated Kiram and the MNLF leadership, according to the same source.
If this is true then it makes perfect sense for President Aquino to be quiet on the Sabah issue, or it might derail his agreement with the Malaysians and sabotage the ongoing peace agreement. And it makes sense for Malaysia, too–they trained the MNLF and the MILF to destabilize the south so the Philippines would not be able to have strength to claim Sabah. They are finally getting what they want by using the MILF as bargaining chip to finally get Sabah.
Unfortunately this is still just one source. It has not been disclosed to any other media outlet or site and the proviso itself is unknown with public officials. This is a secret that Aquino would probably wished to remain secret until the Bangsamoro is ratified and it’s too late to reverse what has been done.
Most probably it’s the Malaysians who’ll wave the agreement around as a trophy (Ha! We got what we wanted! Right under your very noses!). Aquino has not only surrendered to the MILF, he has surrendered to the Malaysians.