Well, I guess I'll leave this post up in case anyone else is having the same problem, but it turns out I'm just dumb and didn't try changing the one setting that was causing the issue :D
For whatever reason, filtering it through the sample rate converter, even if it was set to the same sample rate as the original file, massively increased the bitrate. I took out the filter and all of a sudden I have 900kbps, 48khz ALAC files. Fascinating.