Since Twig uses template path in its cache key, the latter differs when performing cache:warmup for the first or the second time. So I have to run cache:warmup twice in order to get all the templates generated.

At the first run, the service templating.cache_warmer.template_paths fills var/cache/prod/templates.php which contains relative paths like __DIR__.'/../../../vendor/foo/bar/Resources/views/blabla.html.twig'. But at this time the DI container provides a TemplateLocator which has no /templates.php cache file (see constructor) so the var/cache/prod/../../../ part is omitted.

It's only at the second run, when /templates.php exists, that we get a TemplateLocator using these cached paths. In this case, the final cache key is used and templates are properly generated in their final path.