3 gauge romex (NM cable) is *not* rated to 100 amps. It is only rated to 85 amps at the 60c insulation rating (which you are required to use the 60c column for romex). 3 gauge in conduit can use the 75c column which *is* rated to 100a.
The NEC is already very conservative. I have no issues worrying about the safety of an install if done strictly to NEC requirements. I use 6 AWG in EMT conduit and I have never felt the conduit being warm.
I am very hesitant to make the argument about loss being lower to the point where it pays for larger gauge wire. It depends on a LOT of factors. If you spend $800 a year on power AND you can make the argument that you get 1% *less* loss with larger wire (which I question for most installs if that is feasible) then that is only $8 a year. If you spend $100 more in wire, that is a pretty long payback (not even factoring in time value of money).
Now with that being said, I often am a fan of increasing wire sizes for future proofing and for the other reasons listed above, but I don't think it is necessary for safety and I am not sure about the ROI on the wire upsizing just for that reason.