Well first, milspec vs. commercial tends to become important when you're talking about a duty/patrol AR. Something very similar to the military M4 (or sometimes M16) but usually a semiauto version. When talking about a target or varmint AR there can be advantages to deviations from milspec. Some deviations from milspec are considered good even with a patrol rifle, things like midlength gas on a 16" barrel and a cold hammer forged barrel. But barrel twist rate (1:7"), chrome lining, barrel steel, high pressure testing and MPI testing should be milspec. Same goes for the BCG - proper materials, chrome lining, HP/MPI, shot peening and proper staking. Those are the most important things I can think of.
As far as sizing, the commercial diameter receiver extension is larger than the milspec version. This is outside diameter so milpsec stocks won't fit on a commercial tube. Commercial (A2) sights are 0.04" shorter than milspec version so you can run in to zeroing problems if you put a third party rear sight (which are almost always milspec height) on your DPMS.
There's a lot more to it than that but it's a start anyway.
The biggest issue with assembling an AR isn't so much getting the parts together right - it's getting the right parts together.
US Army 1966-69, VFW Life Member, Retired Geek