Can the conflict between the use of a
No. A base element with href attribute affects all URL-valued attributes, by definition. Your page probably needs a redesign. The base element as such is seldom a good idea, and a elements that are not meant to be links are even worse.
Angular $locationProvider html5Mode /
javascript,angularjs,routing,html5-history,base-tag
So, it looks like Angular's inner workings are tightly coupled to the href of the tag which results in major issues if you have a directory structure that's a bit unconventional like mine. Stumbled across this Github thread where people are asking for a feature to change this and @greglockwood...