Great summary. The 'don't roll your own crypto' argument is mostly just shorthand to 'defer to the opinion of experts, use ready-made constructs when possible, and if not, then exercise caution when hooking crypto primitives together in unproven ways'. djb is without a doubt a crypto expert and his NaCl library provides sane defaults and good interfaces for implementing crypto in your application.
The other relevant tptacek post is 'Cryptographic Right Answers' [1], which suggests using the NaCl default for encrypting (ie. Secretbox [2][3]), so the rclone author is deferring entirely to NaCl for crypto, as it's recommended.
[1] https://gist.github.com/tqbf/be58d2d39690c3b366ad