[Extensions Refactor] Migrate HasWithheldHostPermissions callers

HasWithheldHostPermissions() was moved to PermissionsManager in crrev.com/c3466639. This CL finishes migrating the callers, and removes
the method in ScriptingPermissionModifier.

Bug: 1289441
Change-Id: Id1a254ff8aed16ed6fa86143538c96ded54a0d6a
Reviewed-on: https://chromium-review.googlesource.com/c/chromium/src/+/4004564


Reviewed-by: David Bertoni <dbertoni@chromium.org>
Commit-Queue: Emilia Paz <emiliapaz@chromium.org>
Cr-Commit-Position: refs/heads/main@{#1067727}