If I have a VF for bible:Gal-Col in a commentary, it will highlight all text with those milestones and highlight appropriate references outside those books. The Panel menu initially selects Match all word forms and MER and nothing changes unless you deselect MER first and then the Match...
Thereafter, I can select both of them without changing the highlighting, but if I then deselect the Match... the milestones become highlighted again. Then selecting the Match... will remove the milestone highlights!
Logos 31.3 with my Search panels set to Narrow Reference Matching.