First off, I don't think it's totally unreasonable to compare a #4 lock and #5 lock. Most people understand that your #4 lock is going to play a tighter role in general play and a more supportive role in the lineouts, but I don't believe the initial question on this thread was to determine whether a #4 lock is more important than a #5 lock, it's asking which of Bakkies Botha or Victor Matfield was better at his role and was a more valuable player for the Springboks . . . and in that vein, one could compare a scrumhalf and a prop, never mind two locks.
Now that I've hopefully got the pedants out of the way, I'd like to mention the respective players behaviour and temperament before answering the real question as to which was the better player. In terms of temperament, Bakkies was pretty much an out-and-out thug while Matfield generally conducted himself well on the field, seldom seeking confrontation and even showing some leadership qualities on occasion. As a Springbok rugby supporter, Bakkies often embarrassed me with his oafish behaviour and his insistence on trying to be the tough guy of the team . . . never more so than when he head-butted the smallest player on the field from behind while he was on the ground . . . but that was Bakkies. He saw himself as the "enforcer" of the team - and sadly, young Eben Etzebeth looks as if he's going the same route - which basically meant he'd concede a lot of penalties and free kicks but also made him a yellow card liability. That has to be a factor when weighing up the respective merits of the players and their value to the team.
As a lineout jumper, Matfield had no equal during his playing career and of the locks I've seen, only John Eales can be compared to Matfield in terms of lineout ability. Bakkies was probably the better scrummager and he was also a lot more effective in general play. Matfield's great weakness was his habit of swanning around in the backline instead of getting stuck in and playing to the ball as Bakkies did. It wouldn't have been such a weakness if Matfield was effective with ball in hand, but he had no great pace, penetration or ball skills. Ironically, Bakkies was the better player with ball in hand even if he was probably slower.
If someone had asked me this question before RWC 2011 I probably would have said Matfield was the better player but I will never forget how Matfield (and Schalk Burger) completely stuffed up our backline in the RWC 2011 quarterfinal against Australia. I know there are a lot of crybabies who think that loss was all due to Bryce Lawrence but I'd ask those same excuse-makers to watch that game and count how many times Victor Matfield and Schalk Burger were the first or second receivers in the backline. Please note, I'm not talking about forwards taking the ball up and setting up another phase, Matfield and Burger didn't do that, in that game they actually took on the role of flyhalf or inside centre by trying to beat a man or pass the ball. I know squawkers like Baboon-ou are going to have a fit when they read this and all I'm asking is they count the number of times Matfield and Burger played as backs BEFORE they burst into tears and have a squeal . . . because there's no doubt in my mind that Matfield and Burger lost as that very important game . . . and that's the reason I'm going with Bakkies as the better and more valuable player.