Maybe there is another affected plugin breaking the layout
I took a look at the attached plugins.csv and indeed there is another plugin breaking the layout: Team Foundation Server 5.157.1. Team Foundation Server is known to be incompatible with the Configuration Form Modernization project (see JENKINS-64241). Team Foundation Server has also been suspended due to licensing issues and is not available in new installations (see INFRA-2751). The recommendation is to disable or remove Team Foundation Server.
bloodrxt, can you please confirm that disabling or removing Team Foundation Server resolves your problem? If so, we can close this bug to cover Custom Tools and leave JENKINS-64241 open to cover Team Foundation Server.
Thanks for confirming. Let's keep this bug focused specifically on the problem with Custom Tools and leave JENKINS-64241 open to cover Team Foundation Server specifically. Since the problem with Custom Tools has been fixed, I am marking this Jira issue as resolved.
icoulter and david_hertz, please file a new Jira issue with the tables-to-divs-regression label to cover any issues you are facing, following the instructions on this page to narrow down the problem.