Having resolved my ignorance concerning surface groups I can now answer question 1 negatively (or at least some formulation thereof). It is impossible if Y is an oriented surface of genus at least 2.
Suppose that f:YtoY is a self map of the surface such that the eigenvalues of f∗ acting on each Hi(Y) are all nonzero (otherwise we can't "detect" the betti numbers), and such that Hi(Y) and Hj(Y) do not have eigenvalues of common magnitude for ineqj. Then in particular f∗ acts on H2(Y) nontrivially, say by multiplication by some integer d. This integer cannot be pm1 since then H0(Y) and H2(Y) would contain eigenvectors with eigenvalues of equal magnitude.
Consider the subgroup H=f∗(pi1(Y)) inside G=pi1(Y). If this had infinite index, then f would lift to a map to some infinite covering of Y, so it would induce a trivial map of H2. So H has finite index in G. Let XtoY be the corresponding covering space. Then pi1(X) is a quotient of pi1(Y), hence its abelianization has rank leq2g where g is the genus of Y. This implies that X is a closed surface of genus at most g. But its Euler characteristic is precisely [G:H] times the Euler characteristic of Y, so X=Y. Thus f induces a surjection on pi1(Y). By the post cited above, f actually induces an isomorphism on pi1(Y), so it is a homotopy equivalence. In particular, d=pm1, contrary to assumption.
After writing this it occurs to me that you might object to me ruling out the case d=−1... At any rate, this shows that the eigenvalues can't ever look like they do in the case of the Riemann hypothesis, with magnitude qi/2 on Hi for some q>1.
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