I also ran into the same issues while building a Flutter project but I managed to update the Podfile so that it sets the deployment targets in an automated way:
post_install do |installer|
installer.pods_project.targets.each do |target|
target.build_configurations.each do |config|
config.build_settings['IPHONEOS_DEPLOYMENT_TARGET'] = '12.0'
end
flutter_additional_ios_build_settings(target)
end
end