I think what you're getting at is the construction of the sample space - the space of outcomes over which we define the probability measure (e.g. {H,T} for a coin, or {1,2,3,4,5,6} for a die).

Let's consider two possibilities:

1. Our sample space is "incomplete"

2. Our sample space is too "coarse"

Let's discuss 1 first. Imagine I have a special die that has a hidden binary state which I can control, which forces the die to come up either even or odd. If your sample space is only which side faces up, and I randomize the hidden state appropriately, it appears like a normal die. If your sample space is enlarged to include the hidden state, the entropy of each roll is reduced by one bit. You will not be able to distinguish between a truly random coin and a coin with a hidden state if your sample space is incomplete. Is this the point you were making?

On 2: Now let's imagine I can only observe whether the die comes up even or odd. This is a coarse-graining of the sample space (we get strictly less information - or, we only get some "macro" information). Of course, a coarse-grained sample space is necessarily an incomplete one! We can imagine comparing the outcomes from a normal die, to one which with equal probability rolls an even or odd number, except it cycles through the microstates deterministically e.g. equal chance of {odd, even}, but given that outcome, always goes to next in sequence {(1->3->5), (2->4->6)}.

Incomplete or coarse sample spaces can indeed prevent us from inferring the underlying dynamics. Many processes can have the same apparent entropy on our sample space from radically different underlying processes.