I Don't see how to make an encounter calculator with all the options you have. Sure adding skills, armor, and stats increase difficulty but how each skill and item works together would be a gauge task to determine.
I use level #1 then add and take items or skills. Even in tabletop most gms think Dr encounter building is garbage. It also depends on your players skills, abilities, and play style so an accurate calculator is impossible. This is the main part of being a DM to me second only to telling the story.
So basically use level like cr only ad a guide to not ise to powerful of am enemy. The rest is up.to you to judge. Error on making the encounter on the easy side and have traps or reinforcements ready to apring into action if needed.
A deadly encounter to one group of playeta is easily.for another group the same level and items with good prep time and tactics.
