Lean has independent proof checkers, and Coq could have, too. The fact that these are big systems doesn't harm the de Bruijn principle: you only need to trust the checkers…
(btw I couldn't find the source code for the proof checker in the paper, is it available?)
The fast proof checker I talk about is mm0-c: https://github.com/digama0/mm0/tree/master/mm0-c . It is (deliberately) bare bones, and I'm planning on formalizing approximately the assembly that you get from running that through gcc.
There is a second proof checker for MM0 in mm0-hs: https://github.com/digama0/mm0/tree/master/mm0-hs , which has a few more features like the MM1 server mode to give interactive feedback, as well as a verifier that reads a text version of the proof file (not described in the paper, the .mmu format).
The footnotes are supposed to be links to the github repo but I got the versions mixed up and submitted a partially anonymized version to arXiv.
(btw I couldn't find the source code for the proof checker in the paper, is it available?)