Related Jira ticket referenced in PR incorrectly having their status updated

I am not totally sure I have traced this all back to the correct place but I believe the enabling of [these changes](https://github.com/atlassian/github-for-jira/pull/993) is causing some issues for our org. We have recently started noticing that related jira tickets mentioned in PR body are having the PR being associated incorrectly w/ the related jira ticket. This change in behavior is having a fallout effect of then incorrectly moving the status of the associated ticket in Jira to a state it shouldn't.

Example scenario:
- Working PROJ-**2** jira ticket (`IN PROGRESS`) that is a follow up to already `DONE` PROJ-**1** ticket
- Commit final changes to github for PROJ-2 ticket
- create and submit PR for PROJ-2 and include summary w/ PROJ-2 (how this association use to work) and add a reference to PROJ-**1** in body that is a link like `[PROJ-1](https://myorg.atlassian.net/browse/PROJ-1)` so it is easily navigable by dev reviewing this PR as reference.

expected behavior: PROJ-1 that was already `DONE` remains in `DONE` state. We would also prefer the PR wasn't associated w/ the Jira ticket PROJ-1 as it isn't the PR for that ticket but that isn't a 'huge' problem for us (just adds a lot of noise).

actual behavior: PROJ-1 is auto-moved to `IN REVIEW` even though the PR is actually for PROJ-2

Is there a way to still allow links in PR body so devs can easily click and not trigger this auto-move behavior?

Start by reviewing the changes linked in PR 993 and reproduce the PROJ-2/PROJ-1 scenario using a pull request body containing a linked Jira reference. Compare the association and status update behavior with the expected behavior: links remain clickable without associating or transitioning the referenced ticket.

Written by the indexing model from the issue text.