I wanted to respond to the OP and the basic idea behind this thread. First, Enscheff, thank you for putting this together. Seriously, kudos, it's an interesting discussion for sure.
I do think there are some issues with doing it this way and with your takeaways, which are:
1) You're attempting to objectively measure something using a very subjective ranking/process. The very guys whose opinions you base your values on are the guys telling you they don't really believe in these rankings. Those same guys have pretty much unanimously agreed that the Braves clearly have the #1 farm in baseball, and more than one has said that remains true even if you remove Swanson from the list. So obviously they're not really taking their top 100 or top 200 as gospel and just comparing rankings. Surplus value can be a useful tool to quickly assign some kind of objective measurement to evaluate trades, but it is extremely limited and not nearly advanced or nuanced enough to be used in the way you're trying to use it. It's interesting for discussion, but it is in no way a real determining factor in whose top 200 prospects are better overall.
2) You seem to believe that essentially every prospect beyond the top 200 is worth about the same. I just don't see this as being true, and this is where some of the value in the Braves' farm system comes into play. All these prospect guys have lauded the Braves' depth into the top 30-40 guys in the system, and it is a factor in ranking their system #1. These are guys whose job is to look at prospects and determine their worth, value, or potential impact down the road. You seem to suggest that all of them have about an equal chance of becoming something, but all these prospect guys are telling you that absolutely isn't the case. Travis Demeritte, Derian Cruz, Abrahan Gutierrez, AJ Minter, and on and on...these guys have real value and a much better chance of becoming something down the line than a ton of other players outside the top 200. Sure, other systems have guys like this, but they don't have as many as the Braves do. There is real value in that not accounted for in your valuation.
3) You also seem to believe that basically each player holds similar value to other prospects ranked similarly. While I understand the necessity of this kind of lumping for the purpose of assigning a rough dollar value to ranges using aggregate data, it doesn't really help in evaluating prospects individually or across systems. I've discussed the difference in a 18-year-old at the back end of the top 100 vs. a 24-year-old before, and the point stands. If you have a ranking that has Kevin Maitan and Matt Chapman ranked basically equally (which is certainly possible), it would be insane to suggest they have roughly equal value or that they both enhance their respective farm systems equally. Every team in the league would trade 3 Matt Chapmans for a Maitan.
4) I really don't understand why you continue to harp on the fact that Swanson will drop off soon and nobody on the White Sox or Yankees list will drop off as quickly. Is that really an important distinction to make? Several on both lists will drop off this year, and I think annual evaluations are more valuable and accurate than some kind of rolling list. Plus, you clearly believe that both systems will easily surpass the Braves system soon and won't look back. IMO, this is a biased view that won't hold up. Here are the number of players in each of those 3 systems at each value level (50 or higher) according to BA, with the ages of the guys in those groups:
Braves:
65: 4 (17, 19, 20, 23)
60: 5 (19, 19, 19, 20, 22)
55: 10 (18, 18, 19, 19, 19, 19, 20, 23, 23, 23)
50: 9 (17, 20, 20, 21, 21, 21, 22, 22, 22)
Yankees:
60: 4 (19, 20, 22, 22)
55: 8 (19, 19, 20, 21, 21, 22, 22, 24)
50: 11 (18, 18, 21, 21, 22, 22, 22, 22, 23, 24, 25)
White Sox:
70: 1 (21)
65: 1 (20)
60: 2 (22, 22)
55: 5 (20, 21, 22, 23, 23)
50: 10 (20, 20, 21, 22, 22, 22, 23, 23, 23, 24)
So to begin with (and again, this is obviously just according to BA), the Braves have more top-end talent than either of those two right now, not less. 4 at 65+/9 at 60+, compared with 0/4 and 2/4.
Second, look at those ages. The Braves have 12 teenagers, compared with 5 for the Yankees and 0 for Chicago. The Braves also have just 8 at 22+ (which is usually about prospect peaking time), compared with 12 for the Yankees and 12 for Chicago.
So depending on how you judge a farm system, I guess you can argue one of those might pass Atlanta once Dansby graduates, though most of the prospect guys don't believe that. But beyond that, looking longer-term, how could you try to argue those systems are destined to surpass Atlanta and stay there? If Chicago trades Quintana, that will have an impact, but you could just as easily say the Braves could trade Teheran or Freeman. Neither is likely to happen, but I'm not sure why that matters much anyway. It doesn't change the current state of the Braves system - which is extremely good, incredibly deep, very young, and still stocked with top-end talent.
