I use the 12mm nipples for just about all builds. The decision to round up or down depends on two main factors. The first is knowing the bias of the calculator program and where the spoke is projected to end in the nipple. If the bias is to the short side, or the projected spoke end is below the nipple slot, then go up. OTOH if the spoke is estimated to end above the slot, then your upside may be limited, which brings in the 2nd consideration.

The amount of possible overrun above the top of the nipple varies with spoke & nipple thread length. I use nipples with 7-8mm internal thread, which allows overrun of 2-3mm with standard 10mm spoke thread length. However some nipples have more thread length and will not allow much overrun if any at all. That would argue for rounding down.