Also noted on the corresponding GitHub issue -- the issue here was your syntax in mapping to values:

The values you want to set are: AzureFunctionsJobHost__logging__logLevel__Function.http_trigger.User AzureFunctionsJobHost__logging__logLevel__Function.http_trigger

The key is that underscores map to object traversal within host.json.

Values like Function.http_trigger.User are just strings, so there's no need to replace the periods with underscores.