I would not use baking soda or pine shavings in with the bunny. But you can leave an open box of baking soda up high in the room like you would in your refrigerator to absorb odors in general. Also a dish of coffee grounds, or a piece of charcoal is good for a room odor absorber. None within reach of the bunny however.
I use Aspen pellets and aspen shavings and that has a less pungent smell than pine even, and really absorbs odors very well. You could mix the aspen with the care fresh and see if it works better for you.
Be sure to keep them totally separated, not even cages within inches apart, until the spays are done and another month has gone by. They may be spraying to mark territory, but if either one is not sexed properly and they are together, one could get pregnant really much sooner than you would think. You don’t want an accidental litter, so you really need a second cage.