LD ,I'm not an engineer ,it would never occured to me 2 3 inch beams would be less than 1 6 inch ,
I am not sure what you mean by this??
Some pics, even if in the form of a crappy microsoft paint drawing, would be extremely helpful.
IF you stacked the two 3" beams on top of one another, then no a singgle peice of 6" channel is not as strong. BUT, if side x side, YES, even 5" channel is going to be stronger.
And while capping the sides with 1/4" plate for strength sounds good, it isnt going to add as much strength as you think. Beams get their strength based on 2 main factors, how much mass is at their extremes, and how far appart their extremes are. Look at I-beams, or channel Iron for example. They have a lot of mass at the top and bottoms of the beam. (flanges). And the middle (web) is only their to hold them appart and does little for strength.
A 1/4" x 4" plate doesnt have any mass at the top and bottom edges.
Not to mention that would add another ~3.43lbs/foot to your 3x3, making your side rails of the trailer come in at over 10lbs/foot.
And all of that still would not be as strong as 4" or 5" channel that would weigh half of what that does.
For the cost of your "reinforcement" 1/4"x4", you could probabally just but the channel and be done. Save the 3x3 for crossmembers or another project.