Local configurations not applied when using ConfiguredGraphFactory

When creating Graphs using `ConfiguredGraphFactory`, a `TemplateConfiguration` is used to generate a configuration for each graph. Once a graph is created, its configuration is manifested and can not be changed later on by providing different environment variables.
We noticed this issue specifically when trying to set `graph.replace-instance-if-exists`. According to the documentation, it should be allowed to operate two JanusGraph instances on the same graph and have both use different settings for `graph.replace-instance-if-exists`. However, with `ConfiguredGraphFactory`, this is not the case. Judging from the code, other configuration options are affected as well.

- Version: 1.0.0
- Storage Backend: any
- Mixed Index Backend: any
- Expected Behavior: LOCAL settings are read from environment variables and applied to all graphs
- Current Behavior: Any settings from environment variables are ignored for all graphs
- Steps to Reproduce:
1. Start JanusGraph instance with local setting `key=value1`
2. Create `TemplateConfiguration` with `ConfiguredGraphFactory`
3. Create a graph using `ConfiguredGraphFactory`
4. Shutdown JanusGraph instance and start a new instance with local setting `key=value2`
5. The previously created graph is now still running with `key=value1` instead of `key=value2`.

Start by tracing ConfiguredGraphFactory through TemplateConfiguration creation and graph configuration manifestation. Reproduce the issue with a local setting changing from key=value1 to key=value2 across a restart, then verify that the existing graph uses the new local value rather than the manifested value.

Written by the indexing model from the issue text.