Firstly, GER is also passive.
Secondly, the fact that GER was able to no diff King Crimson during Skipped Time (that only KC supposedly could move in) means that GER is either immune to or can resist time hax. So even an action from the future like The Almighty can be returned to zero.
I know GER is also passive, but Almighty being passive means he doesn't need to take an "action".
King Crimson's situation is a bit different since he had to commit an action to skip time which got RTZ'd. Yhwach doesn't need to do that since he passively nulls it from the future, an action that hasn't actually been done yet so there isn't anything to revert.
For King Crimson: KC being activated to erase time (committing action) -> Time is erased -> GER RTZ (reverting action)
For Yhwach since Almighty is passive: Yhwach stands (committing no action) -> GER doesn't do anything since there is no action being done
Yhwach has resisted Ichibei's conceptual powers along with nulling Orihime's ability which works similarly to GER.
Unless I'm misunderstanding GER (it's been a while since I've seen that fight), then GER shouldn't be affecting Yhwach.
There's also the stat difference. Even if GER worked, would he even be able damage Yhwach?
Even yhwach has to use the ability of almighty which itself count as an action and hence gets stopped by GER. Even if he goes in future GER still will negate yhwach's ability as GER is always active.
The moment he unlocked the Almighty, it was passive. He only lost due to PIS and certain conditions.