You are completely right about the bold part. In the final third of the season, during which we started using the 4-3-3 as our main formation, it was one of the CBs who was moving into the wide areas to close down the first attacker. Then Carrick (or Blind) was dropping deeper to cover for the CB and our FB on the opposite side was moving into the box and nearer to the other CB. So, we had three defenders in the box plus one marking the first attacker, these are the four defensive players LvG desires according to NLMax and other Dutch posters.
I don't believe it was coincidence. There has been a lot of discussion about LvG implementing his philosophy into the first team but we sometimes forget that LvG had to adjust his methods and his preferred style of play to the particularities of the English football too. We must not forget that we struggled in the beginning of the season against sides like Burnley, Leicester, Big Sam's West Ham etc., sides which didn't possess much quality on the ball but they were loaded with pace, strength and incredible energy levels.
Too often we saw players get on the ball in their half and then attempting dynamic runs which cut through our midfield like knife cuts through butter. I believe it was one of LvG's primary concerns, one of the main reasons he started experimenting with different formations and one of the reasons the players seemed so afraid to move in more advanced positions but kept possession in our half instead. The first time we saw this tactic (one CB closing down the first attacker) was in the second half of the away game against QPR. It was mostly Jones who was moving out of position, sometimes in the midfield, to slow down the opposition's attack and give the rest time to get behind the ball. LvG decided to stick with it and it actually paid off.
In that particular tactic the two full backs are indeed in more central positions. The one, as i mentioned earlier, moves in the box to operate as a third CB while the other protects the channel between the (wide) CB and the holding midfielder (who's dropped deeper) with the instruction to track any attacker who attempts a late run in the box or to anticipate a clearance from the defenders and pick up the second balls in between our lines.
A more defensive minded player like McNair might do the job but i'm with you when you say that we could use a more technically gifted RB than Valencia. As you mentioned, it doesn't have to be a dynamic FB, like Coleman, who will always look for the opportunity to do an overlap. If that was the case Rafael would have gotten more playing time. I believe we're looking for a player who will be tactically adequate and play his part in our build up play but also provide some end product in the final third. The fact that none of our FBs could be a threat in the final third was one of the reasons we struggled to create chances last season
I don't believe that van Gaal set it up so that the full backs actually just push up and go into the midfield positions. I believe that this is more down to circumstance than anything else. What I mean by this is that players just fill in for others and, essentially, take up different positions to retain the shape. This is something that's reminiscent of total football where players are able to defend in any area as well. I'll go into detail on this in the next paragraph.
Whenever an opposing winger, attacking midfielder, or wide central midfielder goes out wide in the middle third, Valencia (I'll be referring to him since this is a thread about him) pushes up to immediately press the ball holder out wide and unsettle him. This is down to instruction in order to prevent the wide player from taking the ball and running at our defence and disorganising it. When Valencia pushes up, someone has to take up the right back slot, so Smalling goes there. Someone has to take the central defence slot at the right side, so Carrick/Blind goes there. Since the defensive midfield slot is vacant, Valencia normally drifts into that role whilst Herrera continues to play his usual #8 role. Since the ball's at the right side, the whole team automatically shifts in towards the right to maintain a compact shape (left central defender goes to the middle of the box whilst the left full back goes to the far post; the defensive midfielder at the right side of the defence is normally just beyond the far post to cover for a run into that area).
As you can see, the final positions of the players is a part of his total football philosophy and not something special that he planned out. The issue that we faced earlier, and the reason why van Gaal tried to set us up so that we had 4 players in defence, is that players were moving into areas in between the players' positions, and this caused issues with the players early on as no one took charge of closing down the ball-holder by straying out of their area. This was a real problem for us against teams that played the long-ball game and/or had willing runners in the attacking roles (Vardy, Ings, Sakho, Walters, etc.). van Gaal remedied this by giving certain players the responsibility to close down the ball-holders in those in-between areas, which we saw with Jones/left back on the left and Valencia on the right, and as a result, our whole shape and defensive structure improved; this was because other defenders knew that they wouldn't be the ones challenging for the ball and, instead, holding the shape.
Other than this, though, we'd maintain our usual back 4 shape in the 4-3-3 with Valencia out on the right side in our third marking the opposing wide player. Him being so tough to get past due to his pace and strength made him very useful. Also, his technique and physical traits on the right side allowed us to maintain possession and create spaces in the middle as players would look to close him down. Where he really falls off, though, is his deliveries from the right. If we had a proper right winger instead of Mata, this wouldn't be too much of an issue. However, as seen last season, Valencia cannot be a consistent danger on the right if we play someone like Mata there.