Good question. Looking at that section now, it's pretty unclear. The intention was that bonuses for highlighting or starring a strength replace the bonuses from a lower level. If a bonus doesn't change by highlighting or starring then it's not mentioned, but you still keep it. Taking Crafty as an example:
Crafty
+1d when using environmental elements. +1d when disguising.
Highlight: +2d when disguising. +1d when searching. (And you still get +1d when using environmental elements.)
Star: +2d when disguising, searching, or using environmental elements.
Or Alert:
Alert
+1d when searching. +1d when evading.
Highlight: +2d when searching. When generating a new area or searching, after rolling choose one item. Modify the roll for this item by +/-1. (And +1d when evading.)
Star: +3d when searching. When generating a new area or searching, after rolling on the Random Items table you may reroll one item. (When generating a new area or searching, after rolling choose one item. Modify the roll for this item by +/-1. +1d when evading.)
Although with all of that said if you want to just make every bonus cumulative go for it.