The idea of box-counting dimensions is that the dimensionality of an object can be (somewhat) thought of as dependent on the resolution of the observer.
If I think of the side length of the boxes necessary to cover a figure as a type of "resolution limit", than I imagine that dimensionality of some objects (like a ball of yarn) will vary from one observer to another. Large boxes would imply a very course resolution, while small boxes would imply very fine resolution. From this point of view, the dimensionality of a ball of yarn is $1≤d≤3$ (e.g. the the ball of yarn appears as a 1D object if my resolution is very good, but will appear as a normal 3D ball if my resolution is poor (to the point where I can't discern the individual strings)). (e.g. Every experiment available to that observer will give a result consistent with the ball of yarn being just a 3D ball.)
{\bf Can an observer with low resolution (correctly) claim that a ball of yarn is a 3D manifold? From our view, we know that that the yarn is fundamentally a wound up 1D object, and that the observer's claim of the ball of yarn being 3D is due to the fact that the observer cannot resolve the individual strings? If the yarn is not a manifold, is there a type or class of 'manifold-like objects' that this might resemble?
Can one write a metric or metric-like object (since 'metric' does have a formal definition) where the number of spacial dimensions can be observe-dependent?
A somewhat follow-up question (more physics-centered, so I don't know if it will be answered here) is: can someone then write a theory of gravity (with a Riemann curvature tensor, Ricci Tensor, Christoffel Connections, etc. (or equivalent since this is an unusual scenario)) on a background similar to a ball of yarn which contains a resolution/scale-dependent dimensionality. I imagine it should be possible since in a sense this is the opposite of string theory.
(I'm just going to throw out that I am not trained in mathematics, so I may struggle with formalisms.)
For the most generalized definition of "metric" (a metric space), there is no reason why it cannot be resolution-dependent. A quick crack at it would be the following:
For every $\epsilon > 0$, you have a set $X_\epsilon$, and a function $d_\epsilon: X_\epsilon \times X_\epsilon \to \mathbb{R}$ which satisfies the following three properties for all $x,y,z \in X_\epsilon$:
You would then want a compatibility condition between the different metric spaces $(X_\epsilon, d_\epsilon)$. An idea would be to require for all $\delta < \epsilon$, $X_\delta \subseteq X_\epsilon$, and that $\lim_{\epsilon \to 0} X_\epsilon = B$, where $B$ is your ball of yarn.
Since the $X_\epsilon$ are simply sets, there is no definite dimension to them, and so the dimension (how ever it is defined) can change with $\epsilon$.
You can apply this definition to your example by letting the $X_\epsilon$ be the union of the boxes with side length $\epsilon$, and letting $d_\epsilon(x,y)$ be the length of the shortest path from $x$ to $y$ within the boxes. As $\epsilon \to 0$, the metric space so constructed would be very similar to the metric on (a connected, bounded subspace of) $\mathbb{R}$, while when $\epsilon$ is large, the metric space will be similar to the metric on (a connected, bounded subspace of) $\mathbb{R}^3$. You can make this rigorous with a metric-preserving map from $(X_\epsilon, d_\epsilon)$ to $\mathbb{R}^n$ where $n = 1$ or $3$.
If you take this idea further, you can probably use it to construct a resolution-dependent manifold from the $X_\epsilon$. I, however, am lacking in the expertise necessary for that challenge.