Unless I am missing something- which isn't outside the realm of possibility here- here is the illustrated difference:
Above is a screencap of Larger Starting Squad (irrelevant for this conversation) with Max Squad Size Fix. As you can see, there are 8 slots and for each slot, a soldier is select-able (while only six soldiers are displayed, you have full control over composition and loadout of the entire squad). This is with the .ini edits made to change your starting squad to 6 (6+2) in defaultgamedata.ini and max displayed soldiers to 8 (6+2) in defaultui.ini
This is from Long War Toolbox. I kept the same .ini edits as above, however, LWTB overwrites them back to 4 and 6, respectively, so, when you use LWTB to up the max squad from 4 to 6, you get 8 (6+2), however, they are behind the squad (not a big deal), but, there are still only 6 select-able slots, so, the last two troopers are random and you can't change their loadouts w/o a huge hassle.
Hope this helps and please let me know if I'm just missing something! Love your guys work and I would REALLY like to use LWTB!
*edit* It just occured to me that NOT supporting UI past 6 soldiers may have been intentional on your part because you actually support a squad size of up to 12- and, if this is the reasoning, I can accept that.
**edit number 2** after staring at that screencap for the LONGEST time, I just realized you actually CAN select the guys in the back row. Nevermind. Carry on. Nothing to see here... *whistles***