The custom aliases are not SiteAccess aware. When the SA has some tree_root.location_id set the URL to match must be modified like this:

1. Let's assume the content tree looks like this:
Home
------Tasks
-----------Errors
2. Our SA (called site2) has set tree_root to Tasks Location.
3. When we use options Place at site root now the newly created URL (we entered test) will look like this:

/test

4. We cannot match such URL to our SA: localhost/site2/test will not work.
5. However, when we add required prefix: tasks to test, so the final alias looks like this: tasks/test we will be able to match localhost/site2/test.

As an improvement option to choose SA has been added when creating custom alias to prepend the required path required by certain SA.