refactor(runtime/v2): use AppI.GetStore() to fetch an initialized RootStore (backport #22205)

[mergify]

Description

Alternative to: #22204

---

Author Checklist

All items are required. Please add a note to the item if the item is not applicable and
please add links to any relevant follow up issues.

I have...

• included the correct type prefix in the PR title, you can find examples of the prefixes below:

• confirmed ! in the type prefix if API or client breaking change

• targeted the correct branch (see PR Targeting)

• provided a link to the relevant issue or specification

• reviewed "Files changed" and left comments if necessary

• included the necessary unit and integration tests

• added a changelog entry to CHANGELOG.md

• updated the relevant documentation or specification, including comments for documenting Go code

• confirmed all CI checks have passed

Reviewers Checklist

All items are required. Please add a note if the item is not applicable and please add
your handle next to the items reviewed if you only reviewed selected items.

Please see Pull Request Reviewer section in the contributing guide for more information on how to review a pull request.

I have...

• confirmed the correct type prefix in the PR title
• confirmed all author checklist items have been addressed
• reviewed state machine logic, API design and naming, documentation is accurate, tests and test coverage

Summary by CodeRabbit

• Refactor

  • Simplified store management by removing the singleton store builder pattern.
  • Streamlined command initialization processes for improved readability and efficiency.
  • Enhanced the application interface for easier store access.

• General Cleanup

  • Removed unused variables and import statements for a cleaner codebase.
  • Improved error messaging for better clarity during configuration unmarshalling.

---

This is an automatic backport of pull request #22205 done by [Mergify](https://mergify.com).

[mergify]

Cherry-pick of dd2369d has failed:

On branch mergify/bp/release/v0.52.x/pr-22205
Your branch is up to date with 'origin/release/v0.52.x'.

You are currently cherry-picking commit dd2369daf.
  (fix conflicts and run "git cherry-pick --continue")
  (use "git cherry-pick --skip" to skip this patch)
  (use "git cherry-pick --abort" to cancel the cherry-pick operation)

Changes to be committed:
	modified:   server/v2/cometbft/server.go
	modified:   simapp/v2/app_di.go
	modified:   simapp/v2/app_test.go
	modified:   simapp/v2/simdv2/cmd/commands.go
	modified:   simapp/v2/simdv2/cmd/root_di.go
	modified:   simapp/v2/simdv2/cmd/testnet.go

Unmerged paths:
  (use "git add/rm <file>..." as appropriate to mark resolution)
	deleted by us:   runtime/v2/module.go
	deleted by us:   runtime/v2/store.go
	deleted by us:   server/v2/server_test.go
	deleted by us:   server/v2/store/server.go
	deleted by us:   server/v2/types.go

To fix up this pull request, you can check it out locally. See documentation: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/reviewing-changes-in-pull-requests/checking-out-pull-requests-locally