The way conversions like the 100% lightning to physical on gutsmasher work is:
any and all bonuses from the skill passives connected to Savagery apply to the skill first.
Then the lightning damage is converted fully to physical.
Finally, any gear bonuses to damage types will be applied.
So any lightning damage bonuses you receive from gear or passives in the tree not directly related to savagery will not boost your damage. Only physical bonuses will apply from those. However, the lightning bonus on savagery itself will apply to the damage before the conversion, since all bonuses directly related to the skill happen before gear conversions.
It can be a bit confusing, so think of it like this: any passive that actually connects to savagery will apply its bonuses first, it’s considered part of the skill. any passive NOT connected isn’t considered part of the skill, thus won’t apply once the conversion happens. Gear is the same thing. it happens after the conversion, so lightning bonuses won’t apply, since the skill at that point is physical.