Even if BtS uses the same map files, could the way it places resources be different?
No since all the code that determines how a map is generated, and how the resources are placed, is contained within the CvMapGeneratorUtil.py file. And BtS is using the same one that Warlords does. The frequency of resources is determined by the CIV4BonusInfos.xml file, and again BtS is using the Warlords version. Any sense that there are less of any type of resource is purely imagination, or just plain bad luck.