Activate Communities Settings: "Allow using standard external profiles for self-registration and user creation." in a scratch org config file

It's undocumented but it is available as enableOotbProfExtUserOpsEnable property in the communities settings metadata as of v47 (Winter '20). If you select the Allow using standard external profiles for self-registration and user creation checkbox and then retrieve the settings metadata using this package

<?xml version="1.0" encoding="UTF-8"?>
<Package xmlns="http://soap.sforce.com/2006/04/metadata">
    <types>
        <members>Communities</members>
        <name>Settings</name>
    </types>
    <version>47.0</version>
</Package>

you'll see the following response (redacted below for brevity)

<?xml version="1.0" encoding="UTF-8"?>
<CommunitiesSettings xmlns="http://soap.sforce.com/2006/04/metadata">
    ... 
    <enableOotbProfExtUserOpsEnable>true</enableOotbProfExtUserOpsEnable>
    ...
</CommunitiesSettings>

You should be able to update it.

In addition to identigral great answer, here is the corresponding code for scratch org creation (project-scratch-def.json)

"settings": {
    "communitiesSettings": {
        "enableNetworksEnabled": true,
        "enableOotbProfExtUserOpsEnable": true
    },