So, I'm reasonably sure these interactions work as I am envisioning it based on my knowledge of the rulings surrounding them and clone effects in general, but I'd like to make sure. Would really appreciate a confirmation from a more rules knowledgeable person.
In general, the phrase "exiled card" on Spell Queller's fourth ability refers only to cards exiled due to its third ability in the same pair, and not due to any other ability, including another ability with the same text as Spell Queller's third ability (C.R. 607.2a).
1. Yes, since Spell Queller no longer has the linked ability pair that exiled the card in question.
2. Yes; for the purposes of the linked ability rules, Spell Queller's original abilities are different from the abilities Spell Queller acquires from itself (C.R. 613.1, 613.1a, 607.2a), so that the "exiled card" on the relevant ability Spell Queller acquires from itself won't refer to any cards, unlike Spell Queller's ordinary ability with the same text, which Spell Queller no longer has.
3. Yes. Since Spell Queller and Metamorphic Alteration leave the battlefield at the same time, Spell Queller will still be a copy of something at the last moment it's on the battlefield, so that Spell Queller won't have any abilities from the pair that exiled the card in question by the time it leaves the battlefield (C.R. 603.10a, 603.10, 603.6c, 613.1, 613.1a).
EDIT: Correctness edit after comment 3 was posted.
Scenario 1:
I cast Spell Queller, exiling a spell from the stack. It resolves normally, exiling the spell.
I then cast Metamorphic Alteration, enchanting the aforementioned Spell Queller.
I choose any other creature, and my Spell Queller becomes a copy of it.
My opponent removes the Spell Queller, which is now copying something else, using, lets say Path to Exile.
They are unable to cast the spell originally exiled by Spell Queller due to Metamorphic Alteration.
Correct?
Scenario 2:
I cast Spell Queller, exiling a spell from the stack. It resolves normally, exiling the spell.
I then cast Metamorphic Alteration, enchanting the aforementioned Spell Queller.
I choose to have Spell Queller copy itself when prompted to choose a creature by Metamorphic Alteration.
My opponent removes the copy of Spell Queller, using, lets say Path to Exile.
Due to the rules surrounding copies and paired abilities from the original cards not linking, they are unable to cast the spell originally exiled by Spell Queller due to Metamorphic Alteration.
Correct?
Scenario 3:
I cast Spell Queller, exiling a spell from the stack. It resolves normally, exiling the spell.
I then cast Metamorphic Alteration, enchanting the aforementioned Spell Queller.
I choose any other creature, or Spell Queller itself.
I cast Mark of Eviction on my copy. During my upkeep, the Spell Queller, Mark of Eviction, and Metamorphic Alteration are returned to my hand simultaneously.
They are unable to cast the spell originally exiled by Spell Queller due to Metamorphic Alteration.
Correct?
1. Yes, since Spell Queller no longer has the linked ability pair that exiled the card in question.
2. Yes; for the purposes of the linked ability rules, Spell Queller's original abilities are different from the abilities Spell Queller acquires from itself (C.R. 613.1, 613.1a, 607.2a), so that the "exiled card" on the relevant ability Spell Queller acquires from itself won't refer to any cards, unlike Spell Queller's ordinary ability with the same text, which Spell Queller no longer has.
3. Yes. Since Spell Queller and Metamorphic Alteration leave the battlefield at the same time, Spell Queller will still be a copy of something at the last moment it's on the battlefield, so that Spell Queller won't have any abilities from the pair that exiled the card in question by the time it leaves the battlefield (C.R. 603.10a, 603.10, 603.6c, 613.1, 613.1a).
EDIT: Correctness edit after comment 3 was posted.
Thanks for your help!