LinkItemCollection UI allows users to set "remaining URL" on internal pages. But the API removes it. The problem seems to be in  EPiServer.ContentApi.Core.Serialization.Models.LinkItemNode.

Basically if it can get IContent out of the HREF it will get a new HREF using UrlResolverService.

IContent val = UrlResolverExtensions.Route(_urlResolver.get_Service(), (UrlBuilder)(object)new UrlBuilder(href));
if (val != null)
{
  ContentLink = _contentModelService.get_Service().GetContentModelReference(val);
  Href = _urlResolverService.get_Service().ResolveUrl(val.get_ContentLink(), null);
}