Both of my Accurate molds require that I hold the dipper up against the sprue plate to get good square bases. If I free pour into the holes they mostly end up rounded, so holding yours up to the bottom spout is probably the right way.
Molds are certainly individualistic. My LBT molds all liked to have the dipper held about 1/4 to 1/2 inch above the cavity and free poured to get a good fill. Another Lyman 2 cavity .30 caliber mold needs to have the dipper hard up against the sprue plate.
I know folks love their bottom pours, but have you tried a dipper? I've read articles back and forth on this, but the concensus of the articles and my own experience seem to indicate that while you can get a higher production rate with a bottom pour, you get a higher percentage of good bullets (keepers) with a dipper. So I switched to a dipper for everything.
On the bases, my instinct tells me that as long as the base is concentric it should be okay. After all a boat tail is not a square base (except where it concentrically meets the full diameter portion) and they shoot pretty straight. But - I'd still want square base bullets to be square, if for no other reason than to be as alike to the other bullets as possible.
Hopefully there might be a partial answer to your question among all that preceding blather...