Yes. Klevu Recommendation banners will use the merchandising rules you have configured for Search.
Please note that rules created for Category pages using Visual Merchandiser will not impact Recommendation banners. Only rules created for Search will impact banners.
For example, if you have the banner of a trending product showing on your homepage and you have boosted the brand Nike within Klevu search rules, your recommendation banner will also take that into consideration and you will see Nike products more prominently.