Good question, I've encountered the same situation yesterday with an Ogor's charge ability.
the Ogor ability let's you roll dice equal to the charge roll (in this case it was 11) for each roll of 4+ a mortal wound is dealt.
However. since the UNIT has the ability, and the ability is only triggered once. damage from that one ability (let's say 6 dice were a 4+) would be 6.
Which Gotrek then would change back to 1 damage because of his ability: If the damage inflicted by an attack, spell or ability that targets or affects this model is greater than 1, change it to 1.
I'm quite certain the rules as written are the rules as intended in this case. Since Gotrek is quite strong against a single SOURCE of incoming damage.
So you look at the source of the damage. A single attack can deal 1 damage, a single spell can deal 1 damage. a single ability can deal 1 damage.
So you have to look how many times the Ability gets triggered.
if the ability does d6, 2d6 per model or 12d6 mortal wounds on a 6+ afterwards is irrelevant, because it only triggers once, and therefore it can only deal 1 damage.
Now for the confusion around the MW's =/= damage:
As per the core rules:
MORTAL WOUNDS
Some attacks, spells and abilities inflict mortal wounds. Do not make hit, wound or save rolls for mortal wounds. Instead, the damage inflicted on the target is equal to the number of mortal wounds that were suffered. Allocate any mortal wounds that are caused while a unit is attacking at the same time as any other wounds caused by the unit’s attacks, after all of the unit’s attacks have been completed. Mortal wounds caused at other times are allocated to models in the target unit as soon as they occur, in the same manner as wounds caused by damage from an attack.After they have been allocated, a mortal wound is treated in the same manner as any other wound for all rules purposes.
I.E.
1 Mortal wound equals 1 Damage
This way the rule makes most sense to me. but i'd love to hear what you guys think if you disagree