Its the responsibility of the FFL in NY to ensure the gun and mags are compliant with NYS laws before he does the transfer to the buyer. The shipping FFL (all guns coming into NY must be sent from an FFL, no private party shipments can be sent to NY) carries no responsibility when shipping to another FFL. Many FFL's from other states do not understand this.
The FFL doing the transfer to the NY resident is the one who carries the burden of ensuring the person can legally possess said firearm. Its the same as any other transfer in any other state. The person shipping a gun to an FFL in Kentucky has no legal responsibility other than ensuring the FFL is currently licensed (ATF EZ check). its the FFL receiving the firearm that carries the responsibility of ensuring the receiver is not a prohibited person.
As said by previous posters, the FFL can take those mags and sell them out of state, or swap them with 10 round mags in another gun for a LEO, and then give the 10 round mags to the buyer.
A local shop only orders glocks with full cap mags because they are easier to get than ones with 10 round mags. When the guns arrive, if he sells to a non LEO, he takes out the mags and drops in 10 rounders. The full cap mags he sells online or to LEOs and agencies.