Ever since wildfly-transaction-client was introduced in WildFly 11 the set-tx-query-timeout feature has been broken. This has been covered in a couple of places:
I believe this was resolved with external discussion and other changes. If not, we can revisit the discussion on the JIRA.
However the feature is still broken in WildFly 13 Beta 1. We have created a simple project to demonstrate the issue.
The issue is important to us and we're currently running a variant of the patch in WFTC-40. This is clearly not ideal. We would be willing to and help fixing the issue however we need guidance on how a proper solution would look like. Assuming someone is not already working on this issue.
This is being worked on. The JBEAP-13301 issue is probably the one to watch until an upstream WFLY JIRA appears.