I think broctl install copies the files to .site directory in the order specified by the SitePolicyPath This is probably incorrect. It should instead be in the reverse order of the path specified in the SitePolicyPath
if a modified version of file with same name (eg. drop.bro) is in dir1 and original is in /usr/local/bro/share/bro; broctl install will overwrite /dir1/drop.bro with /usr/local/bro/share/bro/drop.bro when it creates /usr/local/bro/share/bro/.site folder.
In theory when bro is starting, it should have preference in loading /dir1/drop.bro over /usr/local/bro/share/bro/drop.bro but currently /dir1/drop.bro gets overwritten by /usr/local/bro/share/bro/drop.bro when broctl install creates .site folder.