Solution:
⇒, i.e. n has ≥3 prime divisors: Let n=∏piei. Note it suffices to only consider regular pi-gons. Label the vertices of the n-gon 0,1,…,n−1. Let S={p1xn:0≤x≤p1−1}, and let Sj=S+p3jn for 0≤j≤p3−2. (S+a={s+a:s∈S}.) Then let Sp3−1={p2xn:0≤x≤p2−1}+p3(p3−1)n. Finally, let S′={p3xn:0≤x≤p3−1}.
Then I claim
(i=0⨆p3−1Si)\S′
is well-centered but not decomposable. Well-centered follows from the construction: I only added and subtracted off regular polygons. To show that it's not decomposable, consider p1n. Clearly this is in the set, but isn't in S′. I claim that p1n isn't in any more regular pi-gons. For i≥4, this means that p1n+pin is in some set. But this is a contradiction, as we can easily check that all points we added in are multiples of piei, while pin isn't.
For i=1, note that 0 was removed by S′. For i=2, note that the only multiples of p3e3 that are in some Sj are 0,p1n,…,p1(p1−1)n. In particular, p1n+p2n isn't in any Sj. So it suffices to consider the case i=3, but it is easy to show that p1n+p3(p3−1)n isn't in any Si. So we're done.
⇐, i.e. n has ≤2 prime divisors: This part seems to require knowledge of cyclotomic polynomials. These will easily give a solution in the case n=pa. Now, instead turn to the case n=paqb. The next lemma is the key ingredient to the solution.
Lemma: Every well-centered subpolygon can be gotten by adding in and subtracting off regular polygons.
Note that this is weaker than the problem claim, as the problem claims that adding in polygons is enough.
Proof. It is easy to verify that ϕn(x)=(xpn−1)(xqn−1)(xn−1)(xpqn−1). Therefore, it suffices to check that there exist integer polynomials c(x),d(x) such that
xpn−1xn−1⋅c(x)+xqn−1xn−1⋅d(x)=(xpn−1)(xqn−1)(xn−1)(xpqn−1)
Rearranging means that we want
(xqn−1)⋅c(x)+(xpn−1)⋅d(x)=xpqn−1.
But now, since gcd(n/p,n/q)=n/pq, there exist positive integers s,t such that qsn−ptn=pqn. Now choose c(x)=xqn−1xqsn−1, d(x)=xpn−1xqsn−xpqn to finish.
Now we can finish combinatorially. Say we need subtraction, and at some point we subtract off a p-gon. All the points in the p-gon must have been added at some point. If any of them was added from a p-gon, we could just cancel both p-gons. If they all came from a q-gon, then the sum of those pq-gons would be a pq-gon, which could have been instead written as the sum of qp-gons. So we don't need subtraction either way. This completes the proof.