Hopefully this is a good place to add to this with some findings:
First off, for B2W2, the block for Battle Subway starts at 0x21B00 (instead of 0x21D00), but otherwise it's pretty much the same, so just change that and you're good.
0x21D2C was indeed some "Continue" flag, specifically for Single Trains. When I did a full set of 7 wins it changed to 02. I changed the current/record wins to 14 from the info we already had and changed that to 03, and on my next set I got the subway boss (who pops at match #21).
Immediately after unlocking Super Single Train, I changed its current/record wins to 49, and also changed 0x21D36 to 07, and also got the boss at the end of the next set of 7 I did.
For a full list:
Current/Latest Wins:
0x21D08 - Single
0x21D0A - Double
0x21D0C - Multi w/NPC
0x21D0E - Multi w/ Friend
0x21D12 - Super Single
0x21D14 - Super Double
0x21D16 - Super Multi w/NPC
0x21D18 - Super Multi w/ Friend
Record Wins:
0x21D1A - Single
0x21D1C - Double
0x21D1E - Multi w/NPC
0x21D20 - Multi w/Friend
0x21D24 - Super Single
0x21D26 - Super Double
0x21D28 - Super Multi w/NPC
0x21D2A - Super Multi w/ Friend
"Continue" Flag - Should be desired amount of sets completed +1:
0x21D2C - Single
0x21D2E - Double
0x21D30 - Multi w/NPC
0x21D32 - Multi w/ Friend
0x21D36 - Super Single
0x21D38 - Super Double
0x21D3A - Super Multi w/NPC
0x21D3C - Super Multi w/ Friend
You can basically see that they just move in increments of two bytes, with just a single gap between the normal and single trains. I suspect that's the Wi-Fi train stats.
I am currently in the process of confirming the two Double Trains and the Multi Trains w/ NPC but there should be no reason for the rest to be any different.
TL;DR Assuming you have a Super Train unlocked, set it's continue value to 07 and it's current/record wins to 2A and profit. You don't technically even need the record wins but might as well.
Huge thanks to Saternoir for finding the initial data >.<