According to the new IPG, changes to a decklist caused by missing cards can be reverted if replacements are found (3.5) but changes to a decklist caused by marked cards can not be reverted, even if replacements are found (3.8).
These 2 situations seem similar enough to me. Why is there a difference?

Previous answer here.

Gentle reminder inserted, searching forums for your question is never a bad idea. :)

d:^D

Is it still recommended to not deviate here? Not untill the update?

The change is in effect now; we won't issue an updated version of the document until the regularly-scheduled Battle for Zendikar updates. It's not a deviation; if a player replaces Marked Cards and later finds appropriate replacements, they may revert to the original list.

d:^D