Anonymity networks make sense for remote nodes, not local. The monerod runs in the data center and wallets @home or mobile phone. Here you can find some public .onion nodes.
Your linked README is out of date and contains the link to ANONYMITY_NETWORKS. Hint: monerod contains now addresses of I2P and Tor seed nodes. See: add support for i2p and tor seed nodes
--add-exclusive-node is no longer absolutely necessary.
monerod RPC & P2P can be set up as a hidden service and you can connect your monero (GUI|CLI|RPC) wallet to it.
The monerod P2P and blockchain synchronization will continue to be done via Clearnet as well. If any anonymity network is enabled, (inbound connections
--anonymous-inbound and outbound connections
--tx-proxy) transactions being broadcast that lack a valid "context" (i.e. the transaction did not come from a p2p connection), will only be sent to peers on anonymity networks.