Makisu generated image is double the size of docker build

[gschnaubelt]

Describe the bug

1. Used makisu_build and docker build on the same Dockerfile
2. Used docker inspect and see that the makisu image is about double the size

To Reproduce
Steps to reproduce the behavior:

$ cat Dockerfile
FROM openjdk:11-jdk-slim
RUN apt-get update && apt-get install -y netcat curl && rm -rf /var/lib/apt/lists/*

$ docker build -t java11-test-docker.build .
$ makisu_build -t java11-test-makisu.build .

$ docker inspect java11-test-docker.build | grep -i size
        "Size": 406372276,
        "VirtualSize": 406372276,
$ docker inspect java11-test-makisu.build | grep -i size
        "Size": 807171944,
        "VirtualSize": 807171944,

Expected behavior
I expected the images to be very close in size or the makisu generated image to be smaller

Environments

$ type makisu_build
makisu_build is a function
makisu_build ()
{
    makisu_version=${MAKISU_VERSION:-v0.1.11};
    cd ${@: -1};
    docker run -i --rm --net host -v /var/run/docker.sock:/docker.sock -e DOCKER_HOST=unix:///docker.sock -v $(pwd):/makisu-context -v /tmp/makisu-storage:/makisu-storage gcr.io/makisu-project/makisu:$makisu_version build --commit=explicit --modifyfs=true --load ${@:1:${#@}-1} /makisu-context;
    cd -
}

$ docker --version
Docker version 19.03.4, build 9013bf5

$ sw_vers
ProductName:	Mac OS X
ProductVersion:	10.14.6
BuildVersion:	18G103

Additional context
Add any other context about the problem here--environment configurations, logs, etc.

[yiranwang52]

This might be similar to #243 , caused by our lazy approach to hard links.

[kenotsolutions]

I have the same problem and it impacts pods' initials time.

same docker file size 127.25MB with docker build with makisu 217.84MB

Even if I use --compression=size it does not affect from default.