A skull is the bony framing for a head. In a doctor’s office, it’s use is merely as a visual aid or teaching tool. It’s usage as metaphor depends on context. On a bottle of household cleanser, a skull and crossbones warns of poison. On a pirate flag, it means danger. At the foot of a crucifix, a skull and crossbones symbolizes death and Christ’s triumph over death. In the old He-Man animated television series, the archvillain was Skeletor, whose face was a skull, and so could in that context symbolize evil. Your friend, unfortunately, is taking something with many possible metaphorical meanings and giving it one univocal meaning.
The same holds true for this Protestant’s understanding of a cross. The cross of Christ, most clearly depicted as a crucifix (which your friend might very well disdain given his religious background), is a symbol for the righteous. An empty cross, on the other hand, could very well be a symbol of the Bad Thief, who certainly was not righteous. Once again, necessary context and distinction lets us know what a material object signifies.
As for clothes and/or jewelry with skulls on them, a fascination with skulls could be problematic. Many people who use them these days for personal decoration do so because of an unhealthy interest in death. If you have a lot of clothing and/or jewelry with decorative skulls, you may well want to reassess whether you should continue to adorn yourself with skulls.
