I'm trying to replicate on my party members, and I'm not seeing the large red "negated" text in the attack roll. It may be Spell specific. I had my PC on high ground, shadowheart shooting a crossbow from low ground. Shadowheart hiding negated the low ground. I enwebbed my PC and Shadowheart's aiming percentage estimate showed two green arrows, one red arrow, but the hit percentage is not adjusted for having +1 advantage. I am currently unable to replicate the situation described in my previous post (everything is dead), so I will have to start a new playthrough.
This is working correctly, at least according to 5e RAW. The hit percentage should not be adjusted for having "+1 advantage;" any amount of Disadvantage cancels out any amount of Advantage to a normal roll.
Definitely let us&Larian know if you find a situation where advangage/disadvantage are subtracted to result in "+1 Advantage."