Once I figured out how to write my own addons for this, I was quite pleased with the results.
I had some mods like VaultWiki and CES Site News which use customized forumdisplay and showthread URLs. Using global_setup_complete to update the "exclude forums" option, I was able to save those forums until the addons ran, so resources weren't wasted and 2 versions of their links weren't added.
Also, I had to write an addon for Project Tools, because apparently there wasn't one. Depending how many people actually need that, I may contribute it, but it currently has my custom URL format (/projects/id/, /issues/id/, /milestones/id/) hardcoded.
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