I got this tech note straight from Armalite three years ago when I asked them the same question.
Technical Note 1: MILSPEC RIFLES
The purpose of this Technical Note is to explain Armalite's conformance to MIL-R-63997, the MILSPEC for the M16A2/M-4 Rifle.
1. All claims from any manufacturer that they produce commercial rifles fully in conformance with the MILSPEC are false. Only M16A2/M-4 rifles produced by Colt or M16A2 by FNMI, and accepted by the Army's Tank Automotive and Armaments Command fully meet the requirements of the MILSPEC, and they are not legally producible for sale to the public. Even Colt brand commerical rifles are not in conformance with the drawing portion of the MILSPEC. In fact, Armalite's rifles are closer to the government designs than Colt's.
2. The M16A2/M-4 rifle is manufactured in accordance with MILSPEC MIL-R-63997. A MILSPEC(military specification) describes a product. There are two key elements to a MILSPEC; a verbal description of what the product is and does, and a list of reference documents governing production of the product. In the case of the M16A2, the key document is drawing 9349000, which is a package of drawings setting forth the dimensions and tolerances for the M16A2 rifle.
3. No commercial, semiautomatic rifle from ANY manufacturer meets both the verbal descriptions of the M16A2/M-4 and the technical drawing package.
4. Armalite does not claim that it's rifles are made to the full provisions of MIL-R-63997. All Armalite/Eagle Arms rifles, however, are manufactured to the written requirements set forth by MIL-R-63997.
5.Armalite and Eagle Arms rifle parts feature excellent interchangeability with MILSPEC M16A1/M16A2 and M-4 parts. with the exception of parts designed for semiautomatic use only, no known incompatibilites exist.
CONCLUSION: Claims to production of fully MILSPEC rifles are untrue, and should be regarded with considerable suspicion