A roll of a 1 is always a fail for a saving throw, regardless of whatever modifiers are applied, that is a rule.
In this system (I'm unfamiliar with WHFB) modifiers such as AP-3 and +1 cover are not applied to the save, but to the roll.
The Termi still has a 2+ save, but because you are subtracting 3 from the roll (AP-3), you actually need the D6 to display a 5+.
However, you are also adding 1 to the roll (cover) meaning you need a roll of 4+.
Just remember that modifiers are applied to the roll, not the save, and that they are applied simultaneously and you should be fine.
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