It’s not that weird if you consider that I2PSnark, Hidden Services Manager, and even the Router Console are actually separate applications, which will run only after I2P itself is successfully started. Starting them before I2CP is available would not make sense in the same way that allowing Tor Browser to fetch pages before a SOCKS proxy was available would not make sense. The result is that you start with what we call a “monolithic” config file where all the stuff is stored in one file, called clients.config and i2ptunnel.config respectively, which is immediately migrated to a directory config on most platforms. We did it this way because the monolithic config files are still used on places where the base config directory(/usr/share/i2p) and the working config directory(/var/lib/i2p/i2p-config) are the same which includes Android and Portable installations, so this way we still only need to maintain one config file.
However, if a directory config is already present, the migration will not occur. So if you just drop all your custom I2P config files into /var/lib/i2p/i2p-config they won’t be migrated from the defaults in /usr/share/i2p, including router.config. Everything you don’t include in that config(keys, etc) should be regenerated at runtime, and if it doesn’t file an issue and we’ll take care of it on our end.