  While high stellar obliquities observed in exoplanetary systems may be
attributed to processes that tilt the planetary orbits, it is also possible
that they reflect misalignments between protoplanetary disks and stellar spins.
This latter hypothesis predicts the presence of co-planar multi-planetary
systems misaligned with their central stars. Here we re-evaluate the evidence
of such an architecture that has been claimed for the KOI-89 system. KOI-89 is
an early-type star with one validated transiting planet KOI-89.01/Kepler-462b
(period 84.7 days, radius $3.0\,R_\oplus$) and one transiting planet candidate
KOI-89.02 (period 207.6 days, radius $4.0\,R_\oplus$), where the latter
exhibits transit timing variations (TTVs). A previous modeling of the stellar
gravity-darkening effect in the transit light curves inferred a high stellar
obliquity of $\approx70^\circ$. We perform a photodynamical modeling of the
Kepler transit light curves, and use the resulting constraints on the orbital
configuration and transit times to update the gravity-darkened transit model.
As a result, we find no firm evidence for gravity darkening effect in the
transit shapes and conclude that stellar obliquity is not constrained by the
data. Given evidence for low orbital eccentricities from the dynamical
analysis, the system architecture can thus be consistent with many other
multi-transiting systems with flat, near-circular orbits aligned with the
stellar spin. We find that the TTVs imparted on its neighbor imply that
KOI-89.01 has a mass $\gtrsim20\,M_\oplus$. This would render it one of the
densest known sub-Neptunes, mostly composed of a solid core. Lower masses are
possible if the TTVs are instead due to an unseen third planet.
