The extra dependency files are put into different places than the extra object files' location. Therefore, the rule must pre-make two directories.
../libwrk/$(TARGET)/%.o: %.c | ../libwrk/$(TARGET)
$(COMPILE_recipe)
-$(EXTRA_OBJPAT): $(EXTRA_SRCPAT) | ../lib
+$(EXTRA_OBJPAT): $(EXTRA_SRCPAT) | ../libwrk/$(TARGET) ../lib
@echo $(TARGET) - $(<F)
@$(CA65) -t $(TARGET) $(CA65FLAGS) --create-dep $(@:../lib/%.o=../libwrk/$(TARGET)/%.d) -o $@ $<