Do all unfavorable art. 59 circumstances weigh the same on the base penalty?
In this calculator, yes, by default: each unfavorable factor adds 1/8 of the gap between the offense's minimum and maximum penalty, but that fraction is just an editable starting point. In actual practice, a judge can give different weight to each circumstance, as long as each one is individually justified (CF art. 93, IX).
Can a mitigating factor zero out the sentence?
No. STJ Súmula 231 bars a mitigating factor from reducing the sentence below the statutory minimum set for the offense, even if the mathematical sum of the mitigating factors would produce that result; the 1st phase's legal floor is the absolute limit in the 2nd phase.
Do two special-part causes of increase add up?
Not when they belong to the same group: CP art. 68, sole paragraph, requires applying only the largest fraction among concurring special-part causes of increase (or decrease), discarding the others in that same block. General-part causes, on the other hand, add up normally among themselves and with the largest special-part one.