I found that this had to do with changes in colorspace handling and managed to get some of the things (like linear gradients) back to working order. However, I can't seem to get alpha channel extraction to work right. I reduced the problem to the following:
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my $img = Image::Magick->new;
$img->Read("File_With_Alpha_Channel.png");
my $alpha = $img->Clone();
$alpha->Set(alpha=>'extract');
$img->Composite(image=>$alpha, compose=>'CopyOpacity');
$img->Write("new_file.png");