Wrap auto merge parameters update in database transaction

What does this MR do?

As @cat reported in #217908 (comment 352572239), when statement timeout happens on inserting comment in MR, it prevents processing MRs on trains as prematured MRs could be added to a train.

Quoting #217908 (comment 352575414),

• In the merge_requests_controller, we call AutoMergeService with the merge_train strategy.
• This builds the merge train and calls super { create system note }
• Because creating the system note fails, we never get to call AutoMergeProcessWorker
• AutoMergeProcessWorker was supposed to call AutoMergeService.new.process(mr) which calls MergeTrains::RefreshMergeRequestsService.new.execute, which, creates the pipeline, which finally is supposed to create the train ref

This theory totally makes sense. We should handle the merge train gracefully regardless of the infra issue.

Related #217908 (closed)

Screenshots

Does this MR meet the acceptance criteria?

Conformity

• Changelog entry
• [-] Documentation (if required)
• Code review guidelines
• Merge request performance guidelines
• Style guides
• Database guides
• Separation of EE specific content

Availability and Testing

• Review and add/update tests for this feature/bug. Consider all test levels. See the Test Planning Process.
• [-] Tested in all supported browsers
• [-] Informed Infrastructure department of a default or new setting change, if applicable per definition of done

Security

If this MR contains changes to processing or storing of credentials or tokens, authorization and authentication methods and other items described in the security review guidelines:

• [-] Label as security and @ mention @gitlab-com/gl-security/appsec
• [-] The MR includes necessary changes to maintain consistency between UI, API, email, or other methods
• [-] Security reports checked/validated by a reviewer from the AppSec team