Sample repro:
third_party/WebKit/Tools/Scripts/run-webkit-tests -t gn-debug --additional-driver-flag=--isolate-extensions http/tests/inspector/extensions-headers.html --driver-logging --full-results-html

Affected tests:
http/tests/inspector/extensions-headers.html [ Timeout ]
http/tests/inspector/extensions-iframe-eval.html [ Timeout ]
http/tests/inspector/extensions-ignore-cache.html [ Timeout ]
http/tests/inspector/extensions-network-redirect.html [ Timeout ]
http/tests/inspector/extensions-useragent.html [ Timeout ]

These tests are already disabled for --site-per-process.

The problem seems to be that the DevTools extension page is loaded in a different process from the devtools process.  For the extensions-headers.html test in the repro, the extension is loaded off of http://127.0.0.1:8000//inspector/resources/extension-main.html, while the rest of devtools is apparently at a file:// URL that looks like file:///<path_to_build_dir>/resources/inspector/inspector.html?experiments=true&settings={%22testPath%22:%22\\%22http://127.0.0.1:8000/inspector/extensions-headers.html\\%22%22.  We currently keep DevTools extensions in-process with some longer-term plans for stronger isolation (see  issue 570483 ), but the corresponding check in RenderFrameHostManager::IsRendererTransferNeededForNavigation relies on DevTools being loaded from a kChromeDevToolsScheme, which is apparently not true with layout tests.  The test fails after the extension page tries to access window._extensionServerForTests.sendRequest, which fails because _extensionServerForTests is undefined.

These tests work fine with --isolate-extensions.