So I'm seeing some odd behavior now. I ended up trying the masked_array solution, but I'm seeing breaks in my data at the tile boundaries.

Here's what the data looks like if I use reprojection with just the source band (code: https://pastebin.com/dZVRVKi2): https://imgur.com/WpFKfij

Here's what the data looks like I read into a masked array and use an ndarray source (code: https://pastebin.com/z1xd8mXu): https://imgur.com/2QkQQZf
Ironically enough I get the exact same result with my solution that doesn't use a masked array, but instead modifies the transform: https://pastebin.com/7ph1VYWX