We present improvements to the construction of binary black hole initial data used in the Spectral Einstein Code (SpEC). We introduce new boundary conditions for the extended conformal thin sandwich elliptic equations that enforce the excision surfaces to be slightly inside rather than on the apparent horizons, thus avoiding extrapolation into the black holes at the last stage of initial data construction. We find that this improves initial data constraint violations near and inside the apparent horizons by about 3 orders of magnitude. We construct several initial data sets that are intended to be astrophysically equivalent but use different free data, boundary conditions, and initial gauge conditions. These include free data chosen as a superposition of two black holes in time-independent horizon-penetrating harmonic and damped harmonic coordinates. We also implement initial data for which the initial gauge satisfies the harmonic and damped harmonic gauge conditions; this can be done independently of the free data, since this amounts to a choice of the time derivatives of the lapse and shift. We compare these initial data sets by evolving them. We show that the gravitational waveforms extracted during the evolution of these different initial data sets agree very well after excluding initial transients. However, we do find small differences between these waveforms, which we attribute to small differences in initial orbital eccentricity, and in initial BH masses and spins, resulting from the different choices of free data. Among the cases considered, we find that superposed harmonic initial data lead to significantly smaller transients, smaller variation in BH spins and masses during these transients, smaller constraint violations, and more computationally efficient evolutions. Finally, we study the impact of initial data choices on the construction of zero-eccentricity initial data.