I changed my preferences so that my Notes file uses Sirba GRK, but when I type Bible reference, Logos is changing the font when it creates the link. I didn't notice it because because I used a serif font, but it really stands out now, as you can see.
Also, it isn't possible to change the link font by selecting it and then choosing a different typeface. Notice the difference in the numbers in these serif fonts (I deliberately misspelled "Hebrews" because it changes it otherwise):
None of the font selections in settings make any difference in how the references are displayed.
Any ideas?