When electric, ice, and ground are entered into the Type Coverage Checker, Shedinja goes into "no effect" and Heat Rotom goes into "super effective". If abilities are not factored, Shedinja should go into "normal effectiveness" because electric attacks are normally effective against them. If abilities are factored, Heat Rotom should go into "not very effective" because electric and ice attacks are not very effective, and its only ability is Levitate, which prevents ground attacks. Please be consistent.
Wonder Guard is the only ability that the Type Coverage checker counts, because no Shedinja can exist without that ability. Since that accounts for a whopping 13 immunities, it simply cannot be ignored. Rotom-H on the other hand, while it will always have Levitate, will only be granted 1 immunity by it's ability's grace. So it can be ignored (in comparison). That's just how the Type Coverage Checker works.
Hope I helped!