When you're bulk editing across products, you cannot bulk edit custom field selections -- even if the products you're editing against are in the same product line and are inheriting the same custom fields. The custom fields are only bulk editable as it relates to features when they are within a single product in the filters. If you select multiple products in the filters and the item you want to bulk edit only shows up in one of those products, it works fine. But if it shows up in 2 or more, then the custom fields do not show up. Not a high priority to be able to do this, but I would give it a priority to provide a warning to explain what went wrong so that the user can know why it didn't work.