Considering the spider mastermind is insanely easy, and requires no preperation to deal with here is what i think should be done to fix it.
A: Make the spidermastermind do bullet damage
not only is it intuitive, but it forces decisions, do you waste a spot in your inventory to resist bullet damage that isn't useful until the spidermastermind, or do you have a go with sheer brute force. If bullets make it too easy, make the bullets stronger/more numerous/armour piercing (sperating the 'ignores half armor' from the 'plasma damage' type).
B: spidey has no melee damage
so just let him shoot at close range. This can be special because he is a boss (aracnatrons can stay week to melee), but really going up close to him and getting hit for nothing with just basic red armor makes him a joke boss, and no one likes fighting a joke at the end.