I uploaded the log that shows that I configured the github app as mentioned in the docs but the declarative checkout doesn't work, all other features work. I got it working by manually configuring GitSCM but it's a bad experience after doing so much setup work for the Github app. 

How I fixed it: 
options {
skipDefaultCheckout true
}

stages {
stage('Checkout') {
steps {
checkout([
$class: 'GitSCM',
branches: [[name: '*/main']],
doGenerateSubmoduleConfigurations: false,
extensions: [],
submoduleCfg: [],
userRemoteConfigs: [[
credentialsId: 'ssh-github',
url: 'git@github.com:rootitnow/rootstrap.git'
]]
])
}
}