Dimensional layers matter if those dimensions actually transcend lower ones. There are exceptions like verses which used M-Theory for example (STTGL, ToAru, etc.) with 11-D structures, which doesn´t grant them any cosmological advantage as they can be still affected by the laws of physics across all dimensions, mostly via gravity manipulation and time manipulation. In that case it would be more a question of range to affect those beings, but they aren´t really invulnerable.
I can give you an example from the verse Lessa which even use one RF layer, but in a case of non-transcendence:
Basically, the creator operates from a higher dimensional structure and treat the lower world comparable to a comic/magazine whatever. However, the lower and higher dimensions are connected to eachother, and some physical laws ignore the dimensional boundaries (Which isn´t the case if the dimensions transcend them, because the distance becomes infinity and beyond)
Like you can see here:
Those are temporal dimensions, not even spatial(Which would be still inferior to true transcendental dimensions)
A verse like Honkai Impact for example suffers the same problem:
Those were just two examples. In fact, dimensional superiority isn´t an auto-win. Sometimes it would probably force both sides into a stalemate, as both sides were unable to interact with eachother.
My knowledge on Digimon is too vague, but from what i heard they used fully transcendental dimensions, which means they are superior as a whole, Tenchi Muyo depends on the interpretation. Madoka transcend her multiverse and becomes an Observer which has clearly elements as some higher dimensional entity.
Zeno was able to erase a big part of a timeline iirc, but he still is bound by timelines as every new branched timeline also contained a new Zeno. He clearly has no higher dimensional existence, especially not since he isn´t a Singularity. He also would be still unable to affect those beings, because Zeno lacks of range to affect them.