The Bonus table from page 127 Character Law is an Option, not part of the core rules. If you are not using that option, then you ignore that table. If you are using it, then that means that there will be changes to how you handle other things. For example, you will ignore all other references to level bonuses to skills, and use the bonuses from that table.
Therefore, the table on page 127, IF you are using it, would over-ride the text from Spell Law page 41 (i.e. use the level bonuses from the table, NOT from any other core text regardling level bonuses).
In regards to elemental ball attacks -- there is NO skill involved in making those attacks, only the bonuses as given in Spell Law (and since there are no skills involved, using the table on page 127 would not change how ball spells are cast).