Well the mods have to change then cause I’ve faced the exact same teams earlier in the sector and outsped them easily and now with the same modifiers they all have over 327 speed
Each sector has a bit of info before you access it. Tap on the Sector from the "choose a sector" screen instead of the button that enters that sector.
It will tell you that each squad gets a bonus between x% and y%. The lower and upper boundaries change with each sector. It also says that the exact value, somewhere between X & Y, is higher and higher (but still never exceeding Y) the farther along the sector you go. Presumably on the last node before the boss fight, this bonus is equal to Y%, but we're not entirely sure. It could be that Y% only applies to the boss node.
In any case, even if you meet the same team twice, they won't have the same stats since one team will necessarily be (at least one node) further along your sector path.