The dimension value boost and bury feature works correctly with disabled refinements.

To illustrate the interaction of both features, assume that your query (with disabled refinements being enabled) returns the following:

Dimension X:
  A (disabled)
  B
  C
  D (disabled)
  E
  F (disabled)

You then use the dimension value boost and bury feature. You decide to bury A and boost E and D. The same disabled refinements query would now return:

Dimension X:
  D (disabled)
  E
  B
  C
  F (disabled)
  A (disabled)

When using these features in concert, you must be very careful to provide a consistent user experience in your UI. It is very easy to create a situation where implicitly selecting a dimension value will cause a rule to fire which may decide to boost or bury some dimension values. It is very important for the disabled refinements features that the order of dimension values on the page remain the same in order to present a good user experience. Changing the order (by using the boost and bury feature) may confuse the user. Therefore, in general you should try to make sure your set of boosted and buried dimension values is the same in your default and base navigation queries.