Webgrind is ignoring index.php by default because of the following default setting:
static $hideWebgrindProfiles = true;
This means WordPress, which uses index.php to route all requests, does not show profiles for normal page loads. I wasn't able to find a way to configure this without overriding the config file itself, which isn't a future-proof solution.
In docker, xdebug isn't even installed and webgrind will never profile itself.