Oh, that's is an issue. in our composer script npm install and npm update.
Consider using separate steps in Envoyer, where you install NPM deps, and build your assets. That's only option in your case, since Envoyer, does not support increasing timeouts. Deployment hooks designed right for that actions.
I'm 90% sure this is network related. Maybe, it depends on current server load, when resources heavy used, installs and compilations way slower, than on servers with more free CPU & RAM available.
Of course, i can be wrong, but i suggest you to take a look into at network speed and resources usage on your servers.